Star Trek: The Mass Effect 2
by Jed Rhodes
Summary: Captain Shepard of the USS Normandy is killed in action - and two years later is resurrected by the shadowy Section 31. Given command of a new ship and crew, can he halt the plans of the pure Reapers, or has he returned only to face death again?
1. Death of the Normandy

**AN: So, here we are. Started writing this second half while I was still halfway through the first half. Can't believe I managed to get this far with this story actually, I'm quite impressed with myself. **

**One small note before we begin: there was a tendency reviews to be left that were unsigned but had very specific queries/issues with the story that I felt required a reply, however doing so in Author's notes cluttered up the story and artificially inflated the word count, something I intend to avoid as much as possible in this story. Without wishing to be ungrateful for detailed, engaged reviews, I ask that anyone reviewing with detailed queries or points please sign in with an account if possible so I may reply to them personally. I hope this is not unreasonable.**

**Anyway: I hope everyone enjoys the sequel. :-)**

* * *

**Prologue: Death Of The Normandy**

The woman was young, or at least young looking. Her hair was long and dark, her face beautiful in a classic kind of way, and her figure was slim and curvy in the right places, only emphasised by the body-hugging black, grey and purple uniform she wore. Her voice was calm and measured, but the scepticism with which she approached the entire topic of her conversation remained steadfast.

"Shepard did wonders for Starfleet. He basically saved an entire foreign government, putting them in our debt in the process. But for all that, he is only one man."

"I know." The man's voice was sharp contrast, cold and calculated but dynamic as well. His hair was short and grey, his face lined with many years worth of cares. His uniform was red, grey and black, with gold decorations as befitted a man of his stature. "But that one man is our best source of intelligence on the Reapers."

"His history with us makes it unlikely he'll help willingly, you do realise that." She was to trying to be insubordinate, she was merely stating facts.

"Then he helps unwillingly," the man replied sharply. "I only need his help, not for him to be all smiles and cheerfulness when he does it. I outrank him. Worst comes to the worst, he'll have to follow orders. Besides, his experience with us is Reed, and Reed will be working under his command."

The woman nodded, understanding his reasoning. "I still can't believe they're making the _Normandy_ do such boring, routine patrols. They aren't going to stumble onto a new Borg invasion by flying around scanning random systems."

"We know they won't, but they don't. At any rate, the patrols are mainly to appease the Council races, not because Starfleet thinks they're any good. We both know that appeasing the Council races is important, especially given their strength. We need them for the war - for more than one - much as we may not like some of the political requirements for that help." The cold words demonstrated the cool intellect the man commanded, as he calculated the maximum potential strength and benefit that the Council could add to any war with the Borg versus the possibility of success without them. Such calculations were his stock in trade, the thing that made him a formidable leader, and sometimes she was in awe of them, and him. Sometimes, though, he terrified her with the extent of his ruthlessness - an extent that surpassed anyone else in this organisation.

"What about our strength?" the woman asked softly.

"That rather depends on the shipyards, doesn't it." The question was implicit, without needing a real voiced answer (since he probably already knew exactly how well the shipyards were doing), but she knew him well enough to answer it anyway, just to be absolutely certain.

"We're building ships as fast as we can, and there's always crews, so we're getting it done, slowly but surely. I only hope it will be enough when the Borg - and the Reapers - show up again."

Confidence now filled the man's voice, confidence born of more planning and forethought than was strictly necessary even for a worst case scenario - just how Admiral Jack Harper, Starfleet officer and current head of Section 31, liked it. "We will have Captain Shepard, and the best fleet in the galaxy. It will be more than enough."

* * *

Although he had perhaps not had the best time while commanding the USS _Normandy_, given her heavy involvement in the recent Borg incursion and several major battles, Captain John Shepard thought with a vaguely proud - if tired - smile on his face that he had made a reasonably good accounting of himself as her Captain. She was - or rather, had been - an _Ambassador_ class starship, her elegant swan neck and beautiful blue main deflector set into the stardrive section, under a beautiful round saucer section that shone silver-grey in the starlight. It was a shame, he thought to himself, that this service was about to end like this, and more a shame that he was about to die and not be able to relive it in his memories.

It was funny. He had woken up this morning in a surprisingly good mood, feeling as though everything would go well today. He had shaved his stubble for once, deciding to go with the clean shaven look. He had even smoothed down his somewhat untamed hair - he'd been letting it grow out these last couple of months, letting himself get more at ease with being the Captain of a starship. The effect was messy but worth it.

The _Normandy's_ most recent orders had been to fly around some outer sectors of Federation space, performing what were essentially dull patrol duties, or as Jeff Moreau (commonly known as Joker), his helmsman, preferred to refer to them, "the milk run from hell". Boring, but nonetheless useful: these patrols were ostensibly keeping an eye out for any signs of a continued Borg presence. Although their defeat at the Citadel - and the destruction of the Reaper Sovereign - had been a blow to their enemy, Shepard and Starfleet command both knew that continued Borg presence was a real danger, and so Shepard had agreed to take this patrol run. Secretly though, he knew it wasn't the greatest danger - that lay elsewhere.

The Reapers. Starfleet Command had believed him - they weren't fools - but they were sceptical about the buildup of forces Shepard recommended. They were always less than thrilled about military buildup. It couldn't be helped. Anderson was confident he could convince them - but that still left the milk runs.

* * *

That morning, he had been in his Hazard suit down in the Holodeck, running some training simulations with Garrus Vakarian, his turian security officer. Garrus had taken up Shepard's offer of a permanent post on Normandy after the Battle of the Citadel, unlike Wrex (who had decided to return to his people, or Liara, who had returned to her studies of the Protheans), and had become a permanent tactical officer and security chief. He had also taken to joining the Captain in his training sessions.

The Holodeck - one of four on the ship - was one of Shepard's personal favourite tools for training, leisure, and sometimes - as it had been that morning - catharsis. He and Garrus had run a simulation recreating the attack on the USS _Enterprise_, some three years ago, in which the Borg had invaded the ship and assimilated many of it's crew. Shepard had taken to reliving old battles in this way only recently, mainly as a way of taking revenge on the Borg - he knew if he didn't let these feelings out, they might compromise him when it really mattered, and he couldn't let that happen.

He knew feelings of revenge might not be up to Starfleet's strictest moral standards - nonetheless, he had to admit to a certain level of enjoyment in taking the simulated cybernetic bastards down with an equally simulated TR-116, a luxury he had never had during the real events.

He took down another holographic Borg drone with his TR-116, smiling at the sight of it's head exploding. He checked the weapon again, and nodded to himself.

"I think that's all of them, Captain", Garrus said from behind him. He leant against a bulkhead. "You know, I wish I had a few of these. There's a couple of cases I went through during my time at C-Sec that would have been really nice to handle a little differently."

"Such as?" Shepard asked, his curiosity piqued.

"Eh," Garrus grunted softly. "Nothing that interesting. At least, not right now. Most of it's been dealt with. Old grudges and all that."

Shepard nodded. He knew the feeling of keeping old grudges. Hell, they were standing in a replication of one.

"Grudges can be a good thing, Garrus," he said softly, "provided you don't let them consume you. That's why I exorcise my demons here."

"I have no intention of letting them interfere with my work, Captain," Garrus said a little too formally. He did that sometimes - probably an expression of turian military upbringing. He would become a little too formal, as if taking a comment too seriously.

"_Captain_," the voice of Commander Charles Pressly, Shepard's CO, came through the comm system, interrupting the Captain's response.

Shepard tapped his combadge. "Go ahead, Mr Pressly," he said.

"_Hate to disturb you sir, but we've finished our sweep of this sector and are moving on to the next,_" Pressly informed him. "_I thought you'd wanna be present._"

"Understood," Shepard replied. "I'm on my way now."

He turned to Garrus and shrugged. Garrus returned the gesture, and together, Shepard still in his Hazard suit, the two walked off the Holodeck and headed for the bridge.

* * *

Once they got there, Pressly gave up the command seat with a soft smile. He was a slightly older man, with a goatee and a receding hairline. "All yours, Captain," he said, moving to an auxiliary station nearby that he usually sat at when or being called upon to hold the bridge.

Shepard sat down in the command chair, and began reading over a ship status report summary a crewman handed to him. Nothing seemed too out of the ordinary - _Normandy_ tended towards being more reliable and efficient than the average _Ambassador_ class starship, a combination of many different factors.

"You heard about the Dominion?" he heard Joker say to Kaidan Alenko, Shepard's Ops officer, as he inputted commands into his console. "They're making noises about war."

"Of course they're making noises," Kaidan replied dismissively. "They've wanted a war for years. Only thing stopping them was the presence of the Citadel Council on our side."

"So why now?" Joker asked.

"Combination of our losses and the Citadel's," Kaidan explained, frowning softly. "Plus I heard they might have been building up themselves."

"You seem awfully well informed, Mr Alenko," Shepard interrupted, a teasing smile on his face. "Secret SI plant, are we?"

"No sir," Kaidan replied with an easy grin. "Just motivated to do my homework. We're in enough trouble with the Borg without some other alien empire choosing now to start a war."

"Ain't that the truth," Shepard sighed, sitting back in his chair. The Dominion situation was one he had been briefed about by Anderson and others, including Admirals Ross and Hackett. It was a worry - not that they couldn't defeat the Dominion, troubling though the projections for any conflict were - but rather that they'd be too busy fighting a war with the Dominion to be able to fight against either a renewed Borg invasion or worse, against the Reapers when they finally came.

"So tell me, Mr Alenko," he said, shaking these grim thoughts off. "Is this system any less of a boring patch of nothing than the last three systems?"

In reply, the Ops officer pulled up a list of statistics onto his station.

"Twenty five million particles of space duster cubic metre on average," Kaidan recited, "with an asteroid belt, and a class four comet flying through. No inhabited planets. One class M, early-ish stage of development."

"Early-ish?" Joker snorted. "That a technical term?"

"Yup," Kaidan smiled back. "Acceptable scientific label. Followed by the middleish, and the endish."

"And where's Earth?" Joker asked, a wry eyebrow raised.

"Probably in the middle-ish," Kaidan said with a shrug and a wry grin of his own.

Shepard basked in this - the camaraderie of a team at work. In all his years, he had never had an experience quite like being the a captain, getting to command the machine instead of being the cog, but more importantly seeing the cog at work from outside, it was wonderful.

Little did he know it was all about to end.

"Captain," Garrus said from the tactical station, his hands flying over the console, "I'm picking up an unknown signature, coming in from the edge of the system. It's on an intercept course -"

An explosion shook the bridge, and a second. For a moment, for Shepard at least, the world went black.

* * *

Shepard's world was nothing but darkness for what felt like an eternity at the time - in retrospect, a rather funny thought, given what was about to happen. When he finally he woke up, for a moment he didn't know what had happened. Whatever had hit the _Normandy_, it had hit them with such force that it caused several overloads in the consoles, leaving people dead and injured around the bridge and smoke in the air. Shepard had been thrown out of his chair by the force of the impact, and groaned as he realised he had bruised several ribs in the process. Near him, Pressly was down, the nasty, bloody tear across his jugular and the shrapnel lodged in his eye more than enough to convince Shepard that his redoubtable XO wasn't going to be getting up again. Cursing at losing a good officer - and more importantly, a good friend - Shepard pushed himself to his feet.

The bridge was wreathed in smoke and flame. A lot of people were down - too many.

"Report!" he called. There was no answer, and he snarled slightly. He couldn't deal with no answer, not right now. "I said report!"

After a moment, Kaidan appeared out of the smoke and fire. There was a gash on his forehead but he was otherwise unhurt. He struggled to get to his station for a moment, and finally got into his seat. Next to him, Joker was wrestling with the helm, trying to keep the ship level.

"We've been attacked - whatever hit us, it took out eighty percent of our shields and tore through our hull, which knocked out most of our main power reserves," Kaidan reported, his face a mask of worry as he frantically inputted commands. "Dammit! We're venting atmosphere - and crew!"

More death. Shepard cursed softly under his breath. He hated losing people under his command, and since he had become Captain he had lost thirty six people, many in battle against the Borg - including Ashley Williams.

"Helm control is gone," Joker reported, sounding oddly calm given the situation. He was clearly trying to regain control somehow.

"Any idea what hit us?" the Captain asked his officers.

"I think it was some kind of concentrated particle beam," Kaidan replied, checking his sensor logs. "But I can't be certain."

Shepard frowned - a concentrated particle beam? Sounded like the weapon Sovereign had used on several Starfleet ships during the Battle of the Citadel, but he had to know for certain. "Can you tell me what..."

"_Captain!_" the voice of Tali'Zorah vas Normandy, Shepard's quarian Chief Engineer, came through the comm system, cutting him off. She sounded worried and frantic. "_That hit seriously damaged our warp containment field, and it fused our ejection system._"

"No way to override?" Shepard asked, realising what this meant.

"_None sir, they knew exactly how to hit us,_" Tali said grimly. "_I estimate we'll have a warp core breach on our hands within the next six minutes!_"

"Shit!" Shepard swore, thinking quickly. "Where's the hostile?!"

"No sign of him, though sensors are pretty beat up," Alenko said, tapping out commands on his console. It mostly failed to respond. "He might have shot us up and run."

"That'd be clever," Shepard said grimly. There was no chance of the hostile getting caught in the warp core explosion this way, and there was no need to deal any further damage with the containment rupture. "Alright, let's get the hell out of here." He tapped a command on his armrest console. "All hands, this is the Captain. I am initiating General Order Thirteen, we are abandoning ship. Report to escape pods and shuttles."

Kaidan and Joker turned to look at Shepard. Neither of them had expected him to order an abandoning of the ship, even with the damage they'd sustained, but he looked pretty serious. Slowly, Kaidan got up, and headed for the escape pods, joining the few other bridge crew still alive. Joker on the other hand stayed resolutely where he was, anger on his face. He returned to his console, trying to get it to respond. For the moment, Shepard was content to let him do so. He made certain that every other crewman was off first, triple checking the launch protocols of the shuttles and escape pods as they went.

Eventually, it was only the helmsman left on the bridge. He was still messing with the console, clearly still trying to keep the ship going somehow.

"Joker, move!" Shepard yelled.

"I'm not leaving," the helmsman replied stubbornly. "I won't abandon the _Normandy_."

"And precisely what are you going to do that can save her?" Shepard asked. "She's suffering a core breach!"

"I can save the saucer section," Joker replied, desperately. "Try and get as far away from the explosion as we can."

It would have been a viable plan had they retained crew, but everyone was off by now. Besides, there wasn't enough power for saucer sep left.

"Joker, we have to leave," Shepard said.

"No, I can save her!" Joker replied angrily.

Shepard cursed, and went to the tactical station, accessing the transporter systems. There was enough power left for maybe one transport, for one person.

"What are you doing?" Joker asked, not turning to look at the Captain.

"Saving your ass," Shepard replied - he had found an escape pod that was launched. Joker apparently realised what Shepard was doing a half second before he did it, and got up to protest - but by then it was already too late, and Joker had been beamed away.

"Right," Shepard said. He checked everyone was off - according to the internal sensors, he was the last life form aboard. Unfortunately, all the escape pods and shuttles had left too, and he'd just used the last power the transporters had left.

"Damn," he swore. Now he _did_ have to separate the ship. He jumped down to the helm station and began inputting commands frantically. Fortunately, the power for life support was still present - just. Shepard quickly began re-routing all the power he could from life support, trying to get enough to jump start an emergency saucer separation. Finally, he manged to get sufficient power to have the ship begin the separation sequence. Shepard heard the clang of the sections separating reverberate through the ship, and smiled softly, as he inputted a command to move the saucer section away from the doomed stardrive section. It responded - albeit sluggishly, given the low power - and he smiled as it moved. Maybe he would be able to save something of his ship after all.

A few moments later, Shepard grabbed onto the console as the entire saucer section shuddered under an immense shockwave. More consoles sparked and Shepard was certain at least some of the inertial dampeners had gone offline. Still - he was alive, and there was something left of his ship at least. He found himself struggling to breath.

"_Warning,_" the computer said, interrupting his thoughts. "_Life support offline. Vessel unable to support life._"

Cursing as he remembered the shunted life support power, Shepard retrieved his pressure helmet from his Hazard suit transporter buffer, and sealed himself in. There was enough oxygen in the suit's storage to keep him alive for a few minutes even after the Normandy's life support totally failed.

He looked up at the static-distorted viewscreen to check the space around him - and froze.

That ship must have been the hostile: it was huge, vaguely cylindrical, and it seemed to be made at least partially of rock. It was heading straight for the _Normandy_, and the Ops station, though it's sensors were all but dead, could still confirm that it was charging weapons. Shepard quickly tried to move the saucer section, enact some kind of evasive patter - but it was to no avail. There was no power left.

A bright yellow particle beam lanced out, crashing into the saucer section. It sheared diagonally across the surface of the hull, splitting the saucer in two. Shepard swore as the structural integrity of the bridge failed, the hull breached, and he was sucked out into space.

Suddenly, he found himself floating in space, his Hazard suit protecting him from suffocating as he floated out into the void. Even as he thanked the stars for his luck, he heard a sudden hissing - and the sound of his suit expelling atmosphere into the void reached his ears, which widened with the realisation that he was about to die.

His life flashed before his eyes - his crew, his friends, his ship - and he had time for a moment of reflection on the events that had led up to this.

His last thoughts, as his lungs burned from decreasing oxygen and his brain started feeling cloudy, were sadness at losing his ship, and regretting that he wouldn't be able to serve Starfleet against the Reaper threat when it finally came.

* * *

"I have good news and bad news," she reported, hands clasped behind her back.

"Bad first," Harper ordered, reading a report as he did so.

"Shepard's ship was attacked and destroyed. We suspect the same individuals responsible for several missing ships. We're working on leads."

"Shepard's status?"

"Reported deceased."

Harper's eyes flicked up to her, coldly assessing her body language.

"The good news?" he asked.

She smiled softly. "We recovered the body after a short while - estimated twelve hours of death. We're preparing the contingency plan. Currently estimating several months for cellular restoration - we won't know the exact number until we undergo a complete exam - with another few for any modifications. Best guess - two to three years out."

"Then we'd best hope we don't need him before then, hadn't we?" Harper said, a wry smile on his lips. "You know what you have to do. Carry on Lieutenant Commander Lawson."

"Aye sir," Miranda Lawson said, nodding formally. She turned and walked out of the Admiral's office.

She had work to do.


	2. Section 31

**Chapter One: Section 31**

There were flashes of thought and memory, feelings of pain, but they were faint. There was no feeling of an afterlife, but there was feeling. Deep within his subconscious he recognised that cognisant thought had not ceased, meaning either he was in the afterlife and it was dull, or he wasn't dead.

The latter would have been preferable.

There were voices too - he couldn't make out speech properly, but he could make out... no, he could make out some speech properly - they were talking about brain activity... no, he couldn't quite grasp it - the voices slipped out from between his mental fingers, and he lost the focus to try and grab them again.

An eternity passed in darkness, with Shepard barely aware that he was even thinking.

Then there was a rumble from somewhere that resonated within his mind. He stirred slightly, feeling something - no, that was his body, he was feeling his own body. Ok. It felt strange, getting used to his own body again, but he could do it.

The first thing he remembered fully, as his eyes strained to open, was pain: the feeling of his lungs in agony, almost feeling like they were on fire, as he tried to breathe non-existent air. He gasped, feeling the air go into his lungs smoothly and clearly - more so than he remembered before, although he attributed that to the fact that he had been suffocating the last thing he remembered.

They must have saved him: a shuttle or escape pod could have transported him aboard, he supposed. That being said, this was considerably larger than any shuttle - more like a Starbase medical bay, but he didn't know how long he'd been out so that didn't worry him.

He slowly pushed himself into an upright position. There were a couple of twinges , like sharp stabs into his ribs, and he grabbed his side as he sat up in an attempt to mitigate the pain. It didn't really work, but fortunately the twinges died down after a moment. He looked around, trying to figure out where he was.

It was a Starfleet room, at least. There was an LCARS panel on the wall and Federation and Starfleet symbols liberally bedecked about the place.

He was in what looked like a hospital bed, dressed in blue hospital pyjamas. Near the bed there was a chair, upon which there sat a PADD, what looked a type two phaser - albeit not a design Shepard had seen - and some clothes that Shepard assumed was a Starfleet uniform. The first thing he reached for was the PADD, which had a message displayed addressed to him.

_Shepard. _

_If you're reading this, you've just woken up with a million questions and no answers. Unfortunately, if you are reading this and not speaking to me in person then I have been called away on urgent business and will be unable to assist you in acclimatising. You should get dressed and head for the station control room. Most of your questions will be answered there. _

_I hope that I will be able to clarify things for you soon._

_Commander Miranda Lawson._

Well, that answered some questions, but it raised a few more. Acclimatising? Exactly how badly injured had he been?

Deciding that he had best head for the control room as ordered, he stood up, slipping out of the pyjamas as he did so. He took the time to examine his body, and found - with a certain degree of surprise - that many of his old scars had disappeared. He frowned at that. No Starfleet medical technique he knew could remove every bit of scar tissue from a body. Nonetheless, here he stood - every scar, from a tiny cut across his forehead as a result of narrowly dodging a swinging Borg drone's arm to the scar from the injury on his arm from the recent Citadel battle, was gone.

He shook his head, deciding to add that query to the list of things he had to ask about - the top of which was his crew. He knew he had lost many of them, but how many had survived?

He began putting on the uniform, but stopped as he examined the garment.

When he had been in command of _Normandy_, the uniform had been black trousers, black boots, a division colour turtleneck shirt over a grey vest and a grey-shouldered black jacket with division colour bands around the arm. The badge had been a solid Starfleet delta over a hollow horizontal rectangle.

This uniform however was different - there was still the black trousers, black boots and grey vest, but instead of a division colour turtleneck there was a grey crew neck shirt with division colour bands running down the front and the arms, over which apparently went a double breasted division colour jacket. The Starfleet insignia on that jacket was a hollow silver outline delta with a gold polygon behind it.

Shepard frowned at the changed uniform. Starfleet was known to regularly update it's uniforms, mainly for the sake of being appropriate to the times they lived in and or the fashions of the day, but he would have heard if a uniform change was imminent as there would have been a requirement for the quartermaster to replicate the uniforms to begin issuing them to the crew.

He brushed it off as a lesser mystery, and fastened the scarlet jacket around himself. He had to admit - the uniform looked good on him.

There was another rumble, slightly more pronounced this time. Shepard frowned - what could that be?

A sudden blaring alarm rang through the station, catching Shepard's attention. A red alert. That meant either the station was suffering some kind of critical malfunction - or worse, that it was under attack from something. There was another rumble, and another. Shepard recognised that feeling for what it was - weapons fire! Grabbing the type 2 phaser and securing it to his belt, he moved to leave.

He stepped out of the hospital room, studying his surroundings and determined to find out what was going on. A handful of crewmen in gold ran past him, obviously too caught up in their station being under attack to pay him much mind. Shepard ignored them and headed for the nearest turbolift.

"Control room," he snapped out tersely - the first thing he had said since waking up. His voice sounded slightly dry but other than that, he seemed fine.

The turbolift ride didn't take very long - whether due to being an efficient turbolift or a short journey, Shepard couldn't tell - and quickly reached it's destination. Once he was there, Shepard stepped out into a large room filled with control panels, some of which seemed burnt out as though there had been explosions: Shepard was uncomfortably reminded of the destruction of the _Normandy_. Something was odd about this room though - for a control room, it seemed pretty sparsely manned. There was a dead man in a blue sciences uniform who had apparently been killed by a shorting console judging from his injuries, a black man in a gold uniform manning a tactical station, and a third man... Shepard could only see the back of his head, which had a mane of red hair that had been grown out several inches. He held a phaser assault rifle in one hand and was inputting commands with the other. The man was wearing Starfleet trousers and boots, but he had a tough, sturdy looking black synth-leather jacket on, gold bands on the cuffs and the old Starfleet symbol emblazoned on the back over embossed writing saying "_Betazed, AR-558, Chintoka, Cardassia_".

He turned, revealing the open front of the leather jacket - upon which his combadge, the same as the new one on Shepard's uniform, was present - and a Starfleet operations-division uniform shirt, grey with gold bands, underneath. He had a slightly haggard face, though less haggard than when Shepard had last seen him, and when he saw Shepard he gave a tired smile.

"Captain Shepard," Lieutenant William Reed said cheerfully. "Good to see you up and about."

Shepard's eyes widened in shock at the sight of Reed, unsure precisely how to process this information. The last - and only - time Shepard had met the man, he had been on a dangerous mission to retrieve data from a monstrously unethical study of the spores of an alien plant for possible resistance to assimilation - an experiment that had caused many Federation colonists distress. Worse, he had claimed to be part of a force that made it it's business to perform such experiments. That he was here meant only one thing.

"This is a Section 31 station," he said softly. It wasn't a question.

"Yup," the Section 31 agent said, his British-accented voice far too chirpy for Shepard's liking. "Got to admit, I was expecting you to punch me in the face."

"Don't tempt me," Shepard said, frowning at the man. "I thought about it, but I'm guessing we have more pressing concerns."

"Damn right we do," the black man said. He turned to face Shepard. "Lieutenant Jacob Taylor, weapons specialist and station tactical officer. This station is under attack by Orion pirates. They're boarding as we speak and as per Sec 31 regs, we need to abandon the station."

"Orion pirates?" Shepard said. "Seriously?"

"They must have been feeling daring today," Reed commented dryly.

"it doesn't matter who's attacking us," Jacob said with a wave of the hand. "What matters is that we get off this station before it's destroyed or captured."

"Ok," Shepard nodded, "I guess that's fair."

"Glad you see it our way," Reed said, rolling his eyes. He turned back to the console. "I'm setting up a remote command to self destruct the minute I send a signal. Everyone else should be off of the station soon, one way or another, leaving just us and some Orions. I trust no one objects to me blowing them up." Here he threw Shepard a pointed look. The Captain shrugged.

"It's expedient, at least," he said, "and Orions can't be allowed to get their hands on Starfleet tech. I'm curious as to why they're attacking a Starfleet station."

"We're remote," Taylor explained grimly. "Near the Terminus systems beyond Citadel space. Prime target."

"The Orions have been getting pretty bold these past few months," Reed added. "Security for remote sectors has been lacking."

"Why?" Shepard asked.

Reed sighed, looking vaguely frustrated. "You have questions, I get that, but now isn't the time."

Shepard nodded grimly, understanding his point.

"I'm surprised," Taylor put in, looking between the two men. "I thought you'd have _more_ questions, like why you're here and where here is."

"I assumed that I was picked up and transported to a Starfleet medical facility - or a Section 31 one, in this case - in time to save my life," Shepard replied, frowning slightly at the thought that these were questions he was expected to have. "That is pretty much what happened, right?"

Taylor and Reed shared a look. Reed turned back to Shepard with a slightly sheepish look on his face.

"It's better if Commander Lawson explains that one to you," he said slowly. "Although you're right - you _were_ transported to a Starfleet medical facility, and we _were_ in time to save your life. In a manner of speaking."

"What do you mean?" Shepard said suspiciously.

"We'll explain more afterwards, or Miranda will," Taylor added. "But right now, we have to get past those Orions and reach the shuttlebay."

Shepard nodded, and the three of them made their way to the turbolift.

"How many crew does this station have?" the Captain asked as they walked. "We'll need to save as many as we can."

"We're a small station, only a minimal crew," Reed replied, his voice clipped and efficient. "Myself, Jacob, Miranda, and seventeen others, including poor old Wilson there." He pointed at the dead science officer. "You'll have passed a few security officers racing to fight the Orion boarders. Can't say they'll have too much luck - we're heavily outnumbered." He sounded unhappy at the thought - his crewmates clearly meant something to him. "Miranda was in a transmission room reporting to Admiral Harper, our CO."

Harper... that was a name Shepard had heard before.

"You mentioned him last time we met," he said. "But I didn't know he was part of Section 31."

"Yup," Reed said. "Actually, he's the man in charge of Section 31, give or take. No doubt he'll have a few words for you once we're done."

"Then let's get off this station so he can," Shepard said, taking out his type 2. Privately he thought to himself that he had his own words to say to the man in charge of the secretive branch of Starfleet.

* * *

The turbolift ride went without incident. Unfortunately, according to Reed the shuttlebay was on the other side of the station to the turbolift, necessitating a walk through several corridors and a cargo bay, no doubt all crawling with Orions. Taylor had taken out his own type 2 phaser to prepare, and Reed was recalibrating his rifle.

When the door opened, they stepped out into a junction. A couple of dead Starfleet officers greeted them, one slumped against a wall with an Orion dagger shoved in his chest, and one woman with a disruptor burn on her back.

"Waller and Danes," Reed said softly, sounding more compassionate than Shepard would ever have given him credit for. "Good people."

Without a further word, he led Shepard and Taylor down one corridor, toward the shuttlebay. He seemed a little grimmer than before. The corridor was messy - stray bulkheads had been blown off of the walls, and there were a couple of boxes strewn about.

As little way down the corridor, the group ran into a couple of Orion soldiers - they wore tough leather and ammo vests, and wielded disruptor rifles. At the first sign of the Starfleet officers, they took cover, as did Shepard, Taylor and Reed.

A few disruptor bursts flew down the corridor, sailing over their heads. Shepard sent a shot back down the corridor that missed the Orions. One of the green skinned aliens got cocky, and stood up, sending a shot that narrowly missed Shepard's shoulder - the minute the Orion stood though, Reed ducked out and nailed him in the chest with another shot. The other Orion looked like he was about to make a move, but Jacob shot him in the head, the phaser lancing straight into the Orion's face and boiling away his eyes. And with that, the Orions were dead and the Starfleet officers could move on.

"Is this the best they can do?" Taylor said, contempt and disgust on his face as they passed the dead Orions.

"Apparently so," Shepard replied softly. This incident reminded him that he was dealing with Section 31, people who were perfectly happy doing anything they deemed necessary to protect the Federation. He wasn't necessarily averse to killing people if he had no choice, but it didn't mean he had to like it. Reed and Taylor seemed to treat it as option one.

"So tell me," he said as they walked. "How long have I been out?"

Taylor and Reed shared a glance. Taylor shrugged and indicated that Reed should field the question. The Englishman obliged.

"What makes you think you've been out for long?" he asked.

"New uniforms for one thing," Shepard replied. "That and your caginess, and you being surprised I didn't ask questions about where I am." He paused, letting the clues he had discerned sink in for the two men. "Has it been a while?"

"You might say that," Reed replied casually. "Hang on, we're coming up to the loading dock."

The loading dock - a large space with barrels and crates aplenty, as well as a couple of high gantries - had a few more Orions in it. Reed fired immediately, taking one down, and Taylor took down another. A third charged at Shepard with a knife, but he blocked the first blow, hit his opponent in the Orion equivalent of a solar plexus and then grabbed his head and kneed him in the face.

The sickening crack told Shepard his opponent wasn't getting up again - Shepard frowned. He hadn't hit him that hard. He looked at his hands - they looked the same, minus the scars. What was going on?

"Not bad," Reed said, bringing Shepard's thoughts back to the present. Any other Orions were dead. "Now we'd better get moving."

The three of them quickly reached the door to the shuttlebay.

"You're the Captain," Taylor said to Shepard. "How do you want to play this?"

"Me and you cover Reed's entry," Shepard replied immediately. Seemed the most expedient course - a little dangerous for Reed, but Shepard felt he could handle it. Fortunately, Reed seemed to agree.

"Good plan," the Section 31 agent said with a nod. Without another word, Taylor took up position on the left of the door, and indicated Shepard should take the right. Reed held his rifle higher, ready to storm the loading dock. Suddenly, the door opened - and an Orion slumped to the floor in front of the Section 31 officer.

In front of the group stood a beautiful dark haired woman, holding a hand phaser expertly: she wore the same uniform Shepard and Taylor wore, in the deep purple of the biotic corps. Her rank insignia made her out to be a Commander. She smiled softly as she saw them.

"Gentlemen," she said in greeting, her voice cool, efficient and tinged with an Australian accent. "Captain Shepard, good to see you up and about."

She held out a hand, and he took it.

"Commander Miranda Lawson," she said, her tone brisk and clinical. "I assume you saw my message."

"I did," Shepard replied. "It raised some questions, but nothing overly important that it can't wait til we're safely off station."

"I'm glad," she replied. She looked at Taylor and Reed. "William, Jacob, we need to go."

At once, she turned and began walking away. Reed was right behind her, and they began talking in the kind of clipped sentences That were the shorthand of officers who had worked together for a long time.

"Other survivors?"

"None. Orions were thorough and brutal."

"What happened to the Orions?"

"I was more thorough and more brutal."

"Aren't you always?"

Jacob fell into step next to Shepard, who was still fairly confused by most of this. The other officer gave him a half smile.

"Don't worry," he said in a quiet undertone. "It'll get easier to deal with. Reed's pretty by the book for Sec 31 and Miranda wants one hundred percent from everything and everyone. They get along quite well."

"I never thought I'd see Reed get along with anyone," Shepard replied, frowning at the two other officer's backs. "They aren't...?"

"What, seeing each other?" Jacob shook his head. "Nah. Badge and uniform first, the both of them."

Shepard nodded, privately thinking that he'd seen how "badge and uniform first" Reed was before, and had no desire to see it again.

Eventually, they reached a small _Danube_ class runabout parked in the middle of the shuttlebay. Miranda led the way in, followed by Reed, Shepard and Taylor.

"Don't the Orions have a ship flying around?" Shepard asked. Reed snorted.

"It's a converted bulk freighter from the 23rd century that they bolted some modern weapons and shields onto," he said derisively. "Powerful enough to break open the defences of a small research station, though that doesn't explain their daring. Slow enough that we could run rings around them in a runabout. We'll be out of the system before their engines even warm up."

"And when they try to follow?" Shepard asked

"Just watch," Miranda said from the helm. "William, is the signal ready?"

"Aye," the Englishman replied with a grin.

"Good," Miranda said, inputting a command. It was time to leave this station.

* * *

From the outside, it looked like this. The small, sleek little runabout flew away from the burning space station. It moved quickly - far faster than the bulky, blocky cruiser that moved to follow it. Before said bulky, blocky cruiser could turn and give chase properly however, a signal was sent from the runabout - more specifically, from Reed's tricorder - to the station, initiating an immediate auto destruct. The explosion caught the blocky Orion ship and blew out most of it's major systems, preventing it from even moving, and secondary explosion tore through the ship, blowing it to pieces.

The runabout, meanwhile, accelerated to warp speed, heading towards its destination - and, one very confused occupant hoped, to better answers.


	3. Illusive Admiral

**Chapter Two: Illusive Admiral**

The runabout was a small grey blur at warp, moving speedily away from the broken station. Miranda entered in a few commands from the helm station, and then got up to speak with Shepard. The Captain was sat in the lounge area of the runabout, privately remembering the last time he had sat in one of these _Danube_ class ships, on the way to Virmire. He hoped that this runabout journey wouldn't lead him to anything quite that depressing - or dangerous.

"I imagine you have a fair few questions, Captain," Miranda said, getting straight to business.

"I do," Shepard replied, looking between her and the other officers, "not least of which is, what exactly happened to me?"

The other officers exchanged glances, which in and of itself told Shepard that he wouldn't like the answer. Miranda took a deep breath before speaking.

"Your ship was attacked by an unknown aggressor," she began slowly. "Most of the crew escaped in shuttles and escape pods, but by the time you thought to do so there were none left. Sensor logs indicate you attempted an emergency saucer sep, but the saucer was attacked by the unknown hostile and sheared in half. You were sucked into space, where ruptures to your Hazard suit caused you to suffocate. You died."

"I was obviously recovered and revived," Shepard pointed out.

"You're half right." Miranda looked as though she had trouble thinking of the exact words. "You were killed. Properly dead. Even had a funeral. Your surviving crew attended it, you'll be glad to know."

Shepard blinked. That was... not what he had been expecting. "I was declared dead? Then how...?"

"A combination of medicinal techniques were used to bring you back to life after your body was recovered," Miranda explained, cutting him off mid-sentence. "Cellular regeneration, gene modification, some cybernetic augmentation..."

She was holding something back, and Shepard could tell.

"What else was there?" Shepard asked, not liking her reticence, especially since it concerned him. He had a right to know what had been done to him.

Miranda sighed, obviously less than happy about having to reveal this Next piece of information.

"We used an experimental technique gained from the Borg to reverse the necrosis of your flesh," she explained, speaking quickly, as though that might somehow make the thing she had said less shocking - and less terrifying. "Nanoprobe injection, roughly sixty eight hours after your death, followed by continued nanotechnological therapy as your body was reconstructed. It reversed a lot of the cell damage but we had to keep you in an induced coma for your systems to stabilise. We aren't sure of any side effects, but you are now at least partially dependant on quasi-Borg implants to sustain your bodily functions."

Shepard couldn't really register what she had just said. It was... it was beyond anything he'd had to deal with. He blinked, once and then again, his mind struggling to come up with something - _anything_ - else to explain this... but nothing was forthcoming.

He felt sick, suddenly aware of some contamination throughout his body - like a virus, or a cancer, in his very being. He leaned over, breathing heavily, trying to quell his heaving stomach.

"Shepard?" the voice of Jacob Taylor spoke, his tone full of concern, and Shepard looked up at the man.

"You..." He swallowed reflexively, trying to calm himself, and looked at Miranda. "You put that... that nanotechnological crap... that Borg _filth_... _inside_ me?"

"It was the only way to restore your body," Reed put in, sitting across from Shepard.

"You made me part Borg!" Shepard said, his voice stronger as his anger grew. "You made me like those monsters!"

"We also made you immune to them," Reed said calmly. "If you remember why I was on Feros, the last time we met?"

Shepard thought back, trying to will his thoughts away from the Borg tech swimming in his bloodstream.

"The Thorian," he said. "It's spores had some kind of anti-assimilation effect."

"More specifically, the spores resist any attempt at assimilation," Miranda clarified. "Our modified probes give off the same bioelectric signature as the Thorian spores to avoid rejection, and the modified spores have been engineered to aggressively attack any foreign bodies that give off a traditional Borg electrical signature - that's something they can't adapt to, since the signature is so fundamental they'd never consider needing to change it."

"To cut a long story sort," Reed finished, "you have all the benefits of Borg tech augmenting your systems - including increased health and infection resistance - without the risk of ever being assimilated."

Shepard couldn't believe that, but he realised that dwelling on... on what was in his system was pointless, even though he felt sick even thinking about it.

"Why?" he asked simply.

Miranda and Jacob shared a look.

"We were ordered to by Admiral Harper," she replied slowly. "It's better if he explains our reasons, rather than me."

Shepard nodded, accepting this for the moment, though he still felt sick.

"And exactly how long was I out?" he asked.

"Two years," Reed replied in a clipped tone. Shepard blinked and frowned at him.

"Two years?" he said in a disbelieving tone. "Are you serious?"

"More than you know," Reed said, his tone utterly serious. "A lot of things happened in those two years, Captain, many of them less than pleasant."

There were a lot of questions that raged through Shepard's mind, but there was only one immediate concern.

"What happened to my crew?" he asked. Before any other worries, he was concerned about his shipmates - his friends.

"Most escaped from the ship," Miranda explained. "There was an inquiry as to what exactly happened, and then after that most were reassigned."

"To what positions?" Shepard asked hurriedly.

"I assume you mean your senior staff?" Miranda asked with a raised eyebrow. "Unless you want six hundred and twenty three service records."

"Just the senior staff will do fine," Shepard replied with a nod.

"Alright, Miranda nodded. She pulled up a PADD and began looking through it. "Garrus Vakarian was reassigned to Deep Space Nine, although the station was lost shortly thereafter in the opening battle of the Dominion War."

"The what?" Shepard interrupted, shocked at this revelation.

"Long story," Jacob replied, shaking his head and looking less than happy. "One of us will fill you in later."

Shepard sincerely hoped so. An entire war was a big thing to miss, after all. He made a mental note to look it up as soon as he got a moment to himself.

"After that he took a position as tactical officer on the Akira class USS _Woden_," Miranda continued, speaking as though Shepard had never interrupted. "The _Woden_ was part of Operation Return, as well as the two Chin'toka engagements and the final push on Cardassia. A lucky ship to survive all of those. He returned to DS9 after the war and remains assigned there today."

Chin'toka and Cardassia - those two names were on Reed's jacket. That may have meant the man had fought in the war - Shepard was curious, but it wasn't the right time to ask about that. Maybe if he ever got to trust the man, unlikely as that happening was.

"What about Kaidan Alenko?" he asked instead.

"Assigned first as chief of security then executive officer of the USS _Vancouver_," Miranda replied shortly. "Took part in several major engagements. Did pretty well for himself, all things considered."

"Joker? Tali?" Shepard asked.

"Lieutenant Morehas do done shuttle runs for the most part since the _Normandy's_ destruction, though it wasn't his preferred career move," Miranda replied, looking through the PADD briefly, "and Lieutenant Commander Tali'Zorah vas Starfleet is currently the chief engineer of the USS _Exeter_."

Shepard nodded. He was slightly confused about Tali taking the title "vas Starfleet" but he supposed he could deal with changes after this long - certainly, it was minor compared to an entire major conflict.

"And what about Wrex and Liara?" he asked finally. "I know they left the fleet, but..."

"Urdnot Wrex hasn't left the Krogan homeworld in almost two years," Miranda told him. "He's apparently trying to rebuild their civilisation."

"Huh," Shepard nodded. It was a bit of a far cry from the merc work he'd been doing but Shepard had no need to question it.

"As for Dr T'Soni, I have no information," Miranda said. "Except that there's no record of her being deceased."

That was less than reassuring, but Shepard supposed he could take small blessings.

"I'm glad they're ok," he said softly. It hurt him more than he realised, returning after two years being dead to find a war had happened and his crew - his family - had moved on. "They've gone on without me."

"You'll be up to speed soon enough, Captain," Reed said cheerfully. "We should be coming up to our rendezvous now."

"Who are we rendezvousing with?" Shepard asked.

"Admiral Harper's flag," Jacob said, smiling slightly. "USS _Eagle_."

* * *

A short time later, the runabout came to a patch of empty space. The small group of Starfleet officers stepped inside the cockpit, Miranda going to the helm and inputting some commands, Jacob and Reed watching the empty space from other chairs. Shepard looked out into the blackness of space and frowned.

"I take it the _Eagle_ isn't here yet," he said. He was surprised when Jacob smirked.

"You're forgetting something, Shepard," Reed said. "I left Feros on a ship called the _Eagle_."

It clicked for Shepard a moment before space started shimmering. A minute later, the sleek form of a refit _Excelsior_ class starship appeared out of nowhere, the words USS _Eagle_ NX 102202 emblazoned on the front of her saucer section.

"NX?" Shepard asked. NX was a registry prefix normally associated with ships that were the first of their class, representing experimental designs.

"There's a hundred different experimental systems on Harper's flag," Reed said, "including the experimental cloak you just saw in operation, a deployable exo-layer of ablative hull armour, a transwarp drive, an EMH Mark XI..."

"In short, she's got so much experimental gear aboard that not putting 'NX' seemed a disservice," Jacob interrupted.

Shepard nodded in comprehension, as Miranda executed a docking procedure flawlessly, her fingers dancing across the LCARS panel.

"Come on," she said, standing up. "I have no doubt Admiral Harper will want to meet with you immediately."

* * *

The corridors of the _Eagle_ were strangely normal - Shepard didn't know why, but being on a fairly normal looking _Excelsior_ class starship was almost more disconcerting than being on board a Starship that wasn't normal, because he might have expected that from Section 31. The crew wore uniforms identical to those Shepard, Miranda and Jacob wore - although Shepard noted that there were a fair few biotic corps personnel in purple, which was unusual since the biotic corps never usually had officers serving on ships.

Once they had gotten on board, Reed had made an excuse and walked off in a different direction to the others, citing a report he had to write. Jacob had also headed off, apparently having duties to perform.

Miranda, meanwhile, walked slightly ahead of Shepard, clearly expecting him to follow. He did so as she led him into a turbolift.

"Deck one, bridge," she said. The turbolift immediately complied. Once the lift was moving, she turned to Shepard. "You'll be meeting with Admiral Harper shortly. If you have any questions related to your being brought back, or what the Admiral wants you to do, those are the questions to ask. I doubt he'll appreciate being pestered about events you could look up in a history file."

Shepard nodded, privately irritated by her manner.

"I'll keep it relevant," he promised. He had no intention of asking questions that would be irrelevant - it might be the only time he had this opportunity.

A moment later, they arrived on the bridge and Miranda stepped out. A dark haired man in a red uniform jacket with three pips stood up, turning to face her with what could only be described as a slight sneer on his face.

"Commander Lawson," he said in a deep voice. "And Captain Shepard. The Admiral is waiting for you."

"Thank you _Commander_ Leng," Miranda replied coldly, emphasising the rank ever-so-slightly. "We were just going to meet him now."

She walked through a door to the left of the bridge, Shepard following, throwing a look at Commander Leng as he did so. The man looked dismissively at him, then the door closed, cutting them off from one another. Shepard dismissed the man from his mind, turning to face where he was going.

They were in a fairly standard ready room - a desk, behind which was a chair, and in front of which were two more. At the back of the room a large viewport. Standing near this, looking out at the blackness of space, was a man. He had short grey hair, long enough to be slicked back at least, and he wore a long black overcoat with red and gold bands over the cuffs. He turned around, revealing that he wore a regular uniform, red with good decoration and Admiral bars, underneath the coat. His face was lined with years and care, and his eyes were cold, electric blue implants.

Miranda was standing crisply to attention, clearly waiting for him to speak.

"Thank you, Commander Lawson," he said in a gravelly voice. "That will be all."

She nodded once and left, leaving Shepard alone with the man, who sat in his chair and indicated Shepard should sit as well. The Captain did so, feeling increasingly uncertain about this entire thing.

"Admiral Jack Harper," the man said as Shepard sat. "Effectively head of Section 31 at this time."

"Captain John Shepard," Shepard replied. "Formerly of USS _Normandy_. Although I expect you already knew that."

"Indeed," Harper said, leaning back in his chair. "I imagine you have a few questions about Section 31."

"A few," Shepard replied. "Although I've been told asking you pointless questions is ill-advised."

Harper chuckled slightly. "Commander Lawson's doing no doubt. Rest assured, I'll answer any important queries you have."

"Then answer me this," Shepard said, leaning forward in his chair. "What _is_ Section 31?"

Harper frowned slightly, all traces of mirth gone from his face. He looked like he was seriously thinking about how to approach the question, which Shepard appreciated - since he needed serious answers.

"As Reed told you when you two first met, Article 14, Section 31 of the original Starfleet charter covers the authorisation of actions that are considered extreme in the case of protecting the state," the Admiral said after a moment. "Many of those actions can be considered illegal."

"I can almost understand that," Shepard said, "provided there's sufficient oversight."

"There is no oversight of Section 31," Harper replied, shaking his head slightly. Shepard frowned at that, not certain he had heard the Admiral correctly.

"You're an Admiral in Starfleet," he pointed out, "so I assume you answer to Starfleet Command and the Federation Council?"

Harper took a deep breath, as though he knew what he was about to say was going to be troubling for Shepard. "No. Section 31 is mine, separate from the rest of the chain of command - I am the 'director', though that rank is more unofficial than it sounds. I decide what actions best suit our goals. I don't answer to anyone - my official Admiralty duties are all but non-existent. Most people in the know tend to look the other way."

"No oversight?" Shepard said with a frown, unhappy at the thought. "That's dangerous."

"In the wrong hands," Harper replied, and here he allowed himself a smug smile. The self assured air the man surrounded himself with was palpable - he clearly had no doubts about himself of his capabilities. "I've proven over the course of many years that I am not the wrong hands."

"So you commit illegal acts and sanction immoral experiments without any oversight or control?" Shepard summed up.

"Yes, because no one else can or will and they need to be done," Harper replied, frowning and gesturing with his hand as he made his point. "Section 31 undertakes those actions so that the majority of Starfleet can keep thinking we live in a happy, peaceful universe, and so that universe can keep seeming that way." He paused for a moment. "Not that many think that way anymore, not after the Dominion War."

There was a pause as Shepard thought about everything Harper had said. He focused on the last comment.

"That war - I've heard a little about it, but not much," he said slowly. "What happened?"

"You'll be able to learn more afterward," Harper said, waving a hand dismissively. "But right now it's more important that you trust Section 31, at least a short while. I've had teams spending two years rebuilding you. I need you to understand that we've done it for a good reason."

"And what reason would that be, exactly?" Shepard replied.

Harper sighed, and leaned forward. "As of now, you have more personal knowledge of what we're facing than anyone else in this galaxy. We need that knowledge if we're going to survive."

Shepard blinked, understanding now. "The Reapers. You mean the Reapers."

"Precisely," Harper nodded. "The intel and experience you have, combined with your command ability, is vital to protecting the Federation from their continued threat."

"Continued threat?" Shepard repeated, horrified. "You mean there's an active Reaper presence in this galaxy _right now_?"

"Exactly," Harper confirmed with a nod. "They've begun attacking the Federation. Section 31 will not allow that to continue."

"What, exactly, have they done?" Shepard asked, leaning forward. He was confused by the whole affair. "They can't be here in force or I'd have been told - hell, I'd have figured it out."

"Specifically? We don't know," Harper replied. "But several outlying Federation or Federation-backed colonies have been destroyed - or rather, their people have been kidnapped, while the infrastructure remains intact."

Shepard raised an eyebrow. That kind of attack was rare - almost unheard of, in fact.

"Some kind of bio agent?" he asked.

"That wouldn't explain the lack of bodies," Harper replied. "No sign of battle, no bodies, no collateral bio-degradation or empty clothes, no structural damage. Like a ghost town. The oddest thing is, it's mainly all-human or mostly human colonies that have been attacked."

Shepard raised an eyebrow.

"Rare," he said. "And the non-humans are left behind?"

"They're usually the only evidence left that anything happened," Harper replied. "All witnesses so far have been dead from unknown weapons fire - or else they blabber incoherently about monsters instead of giving us hard intel."

"Trauma isn't uncommon," Shepard said. This was disconcerting - humans were being specifically targeted, and anyone else was either being killed, or else traumatised by whatever happened.

"It's also unhelpful," Harper said, clearly more frustrated with the frailties of the witnesses rather than concerned about their health. "My intention with you is to give you command of a ship and pit you against the Reapers and whatever proxies they're working through - a small team might have more luck than a large fleet in this case, and in any case, the fleet isn't ready."

Shepard leaned back in his chair.

"Is there any Borg involvement?" he had to ask. After all, the Borg had worked with the last active Reaper they had encountered.

"We don't know," Harper replied, clearly less ham happy with that answer. "I wouldn't have said so, given the MO - the Borg usually aren't so subtle or selective - but we can't be certain. That will be one of the things _you_ need to ascertain."

Shepard nodded, thinking his options over. He didn't trust this man - he seemed entirely too comfortable with breaking rules and with his group being under no oversight but his own - but he also wanted to protect the Federation. It was a difficult combination.

"I'd need to see one of these attack sights before agreeing," he said finally. "See for myself that you aren't lying. I'll also need to see more concrete evidence of Reaper involvement than just your word."

Harper nodded. "The _Eagle_ is en route to just such a sight," he said. "The colony of Freedom's Progress was attacked five hours ago. According to our reports, there are no other starships in the area. It's the closest we've been. I'll send you with Commander Lawson and Lieutenant Reed..."

"Not Reed," Shepard interrupted. "I don't want him on my missions."

"Like it or not, he's one of my best and I'll be assigning him to your mission proper once it's under way," Harper said with a frown. "But for this mission, alright. Lawson and Taylor then. Go down, find out what's been happening."

"Acceptable," Shepard said with a nod. "Understand - if I don't find evidence, I'll return to Starfleet proper and go where _they_ want me."

Harper nodded, accepting this, and Shepard stood up.

"We have guest quarters ready for you for the moment," Harper said. "After that, we'll see."

Shepard nodded, and left the ready room, wanting nothing more than to sleep.


	4. Tali on Freedom's Progress

**AN: you might notice an alteration to the story of ME2 come the back end of the chapter. This is the result of a rather awesome inspiration that hit me at the proverbial eleventh hour and I think works really well. Best bit - it only required a little mild restructuring on my end, so all's well. Enjoy :-)**

* * *

**Chapter Three: Tali on Freedom's Progress**

Shepard didn't like the guest quarters they had assigned to him. They were large, spacious, comfortable, everything he could have wanted... to be honest, he couldn't pinpoint a particular thing he found wrong about them - it was just a feeling. The feeling of _everything_ being wrong, somehow.

Or maybe it was him who was wrong.

He had been dead for two years. Dead. Not even just on a mission, or in a coma, but properly dead, proverbially buried, and probably forgotten. What would his crew make of that? What could they _possibly_ make of that?

He felt alone. Those he called friends thought he was gone forever, and while he hadn't been specifically prohibited from doing so, contacting them would probably be unwise. They had moved on. It wasn't fair to open old wounds, bring up old memories, all or the sake of - what? Feeling alive again? No, he don't think that was fair, and it probably wouldn't work - it would just make him feel more out of sorts, like they had moved on and he was static.

He tried sleeping, but his dreams were haunted by fire and explosions and pain, the death of the _Normandy_, and he found himself lying awake again. For hours he stared at the ceiling of his guest quarters, trying to stop thinking about how much had changed.

"_Captain Shepard,_" the voice of Miranda came through the comm system. "_We're approaching Freedom's Progress. The Admiral wants you geared up._"

"Where's your armoury?" Shepard asked tiredly, tapping his combadge.

_"Deck 3,_" Miranda replied. "_See you there._"

Shepard signed off without replying. He was less than thrilled about the whole affair, but duty called and he, like the good soldier he was, would answer.

* * *

Deck 3's armoury was well stocked - Shepard supposed he should have expected as much from Section 31. When he arrived, Jacob and Miranda were already there.

"I take it you still have Hazard suits?" he asked.

"Better," Miranda said, pointing to a far wall. "We have these."

The suits she pointed to were black jumpsuits made of a sort of ribbed rubbery material that looked both tough and manoeuvrable - each jumpsuit had department colour bands running across the shoulders and down the arms, as well as a Starfleet symbol on the upper arm. There were solid elements to the armour - shoulder plates, forearm and greaves - and Shepard frowned at them as he looked over them.

"The basic jumpsuit is equivalent to a Hazard suit," Jacob said. "But they've been adapted to have customisable armour ports with more solid armour attached - a little trick we got from the Citadel races, and pretty helpful against the solid projectile weaponry preferred by most people out there."

Shepard looked at the suit and sighed. It was too much difference, too soon. He was starting to get really sick of sudden changes.

"I suppose it's too much to ask for a good old Hazard suit?" he asked.

Miranda and Jacob looked at each other, and then Miranda turned back to Shepard.

"Of course, Captain," she said. She indicated a compartment that Shepard opened - inside were seven or eight Hazard suits, adapted to look like the current duty uniform but otherwise very familiar to Shepard. He smiled, and went to put one on.

"There have been some performance alterations," Jacob said as Shepard put the suit on. The other man was putting the new armour on. "The buffer holds twice as much equipment as the older models you worked with, and the ablative armour patches can absorb twice the fire before needing repair. The dermal regenerators are three times as efficient..."

"So basically," Shepard summed up, "it works like my old Hazard suit, but better."

"Yup," Jacob smiled. "You'll find the same can be said for a lot of things here."

Shepard nodded, and grabbed what looked like a TR-116.

"This doesn't look that different," he said.

"It isn't, on the outside," Jacob replied. "Except that it's now got a micro replicator inside, powered by one of these." He pointed to a small battery pack on the side of the rifle. "An old TR-116 had a clip size of about fifteen. This thing has a 'clip' capacity of about sixty before needing a ten second recharge cycle."

"I see," Shepard said. "Is it possible to initiate the recharge cycle early?"

Jacob nodded, pointing to a button on the side of the pack.

"That way," he said, "you can recharge between firefights."

"My thoughts exactly," Shepard replied, smiling. He might not trust Section 31, but for now at least he trusted Jacob. The man had a solid head on his shoulders. That gave the Captain hope that maybe he could adjust to this new environment.

"Captain," Miranda said, interrupting the moment of camaraderie that Shepard desperately needed. "If we're all set we should head for the transporter room." She was dressed in a Hazard suit as well - apparently she preferred the manoeuvrability of the design.

"Good idea," Shepard said, nodding. He out the TR-116 in his transporter buffer, as well as a phaser assault rifle. "Let's go."

* * *

In the transporter room, Admiral Harper was waiting for them, hands held behind his back as he surveyed their readiness.

"A few last minute intel notes before you beam down," he said without preamble. "The USS _Exeter_ left an engineering crew on the planet three weeks ago to help with some problems they were having with an automated mech security force they had. If that mech force is still active, it might be problematic. Equally, it might mean there's still members of the _Exeter's_ crew on-planet to help figure out what happened. Either way, keep an eye out."

"Understood," Shepard said with a nod. He felt like the name _Exeter_ should mean something to him, but dismissed the thought as irrelevant at this time. "I assume I'm in charge of the mission?"

"Yes," Harper replied, then looked at Jacob and Miranda. "You two will follow the Captain's orders as if it were me giving them - clear?"

"Clear," Jacob replied immediately.

"Yes sir," Miranda replied a moment later, perhaps a tad more hesitant than Jacob had been.

"Excellent," Harper said, turning back to Shepard. "You know your mission Captain."

Shepard nodded, and without a further word, he and his team stepped onto the transporter pad. Once they were in place, Harper turned to the transporter operator.

"Energise," he said.

* * *

Freedom's Progress: the place wasn't nearly as inspiring as the name suggested it would be - although Shepard could have guessed that. The design was similar to that of a lot of young colonies - all prefabricated buildings and walkways, all in the same dull white colour scheme that made you want to break open a can of paint or six and throw them at the walls.

Shepard looked around, finding the sight depressing, but he shook those thought away, focusing on his mission. He took out a type-2 phaser, not seeing the need for anything more heavy duty.

"Life sign readings?" he asked. Miranda already had her own type-2 phaser and a tricorder out, and she was scanning the immediate area.

"Hard to get a clear reading," she said after a moment. "There's some kind of interference, I can't get a decent scan."

"Troubling," Jacob said as he scanned the area, his weapon - a phaser assault rifle - out and aimed. "That means anything could be waiting for us down here."

As if to punctuate that thought, a phaser blast impacted near them,vaporising a crate.

"Shit! Cover!" Shepard yelled, jumping behind a wall. A few more shots impacted near the team, but whoever was firing wasn't very accurate. Shepard risked a peek, and saw a figure firing from a gantry outside a prefab - it looked humanoid, male - more importantly, it looked like...

"Hold fire!" Shepard yelled. "We're Starfleet! Starfleet!"

The figure kept firing, but Shepard was sure it was a Starfleet officer - the colours matched up at least - science blue. He tapped his combadge.

"This is Captain Shepard to any Starfleet officers in the area," he said, unsure whether he should transmit the fact that he was part of Section 31. "I am a Starfleet officer here as part of a recon and relief mission. Come in, please."

He waited a few moments, but the Starfleet officer kept firing down at them.

"Alternatives?" Jacob asked. Even as he spoke, Shepard's combadge beeped, and a very familiar voice spoke, still soft and yet harder than when he had last heard it.

"_Captain Shepard, this is Lieutenant Commander Tali'Zorah vas Starfleet._" Shepard's heart jumped, shocked at hearing the voice of one of his old crew. "_What is your situation?_"

She didn't sound surprised to hear his voice - and yet, there were other "Shepard's" in the galaxy, and his voice wasn't all that distinctive. Maybe she thought she was being unlucky, or that it was all very ironic. He realised why the _Exeter_ had sounded familiar - she was the chief engineer of that ship! She must have been left here while the attack happened. He decided to play it cool, not letting on that he was - well, him.

"Shepard to Zorah," he said, "there is a Starfleet officer firing down on my position, looks quarian. What the hell is going on here?"

"_A Starfleet officer?_" Tali replied, sounding confused. "_Nothing else?_"

"No," Shepard said, frowning. "One Starfleet officer, looks to be quarian."

There was a moment's pause before Tali's voice replied. "_Ah. You must have found Ensign Veetor'Nara._"

"Well that's great, what do we win?" Miranda said sarcastically, rolling her eyes as another phaser blast impacted near them.

"What's wrong with him?" Shepard asked, ignoring Miranda.

"_The attack was fast,_" Tali replied quickly, sounding slightly tired but otherwise alright. "_And we lost a lot of friends - he was always... nervous, but this attack... being around things like that is not good for him, and that's not counting any possible damage to his envirosuit. I think he might be delirious."_

Shepard cursed. "Ok. Any other threats I should worry about, or is he it?"

"_The attackers... if you haven't met them, they're gone,_" Tali said quietly. "_It's only Veetor._"

Shepard nodded and turned to Miranda, an idea forming in his head slowly.

"How controlled are your biotics?" he asked.

"As controlled as you can have in a human," she replied immediately. Well, she certainly didn't lack for confidence. "What's your plan?"

"Could you grab his phaser rifle from here?" Shepard asked, jabbing a thumb over at Veetor, who was still firing.

Miranda paused for a moment, considering. "I think so, but you'd need to grab his attention. The Hazard suit won't take more than a couple of direct hits. Of course, grabbing his attention means exposing yourself to his fire..."

"Ok," Jacob put in, "I'll go cause a distraction." He tensed, ready to move.

"No," Shepard said, holding a hand up. "I won't ask you to do that, Jacob." He might not have entirely trusted either of these people, but he was still their Captain here, which in his opinion made the crazy suicide missions his job, and no one else's. "I'll go."

Jacob nodded, not looking entirely happy but not willing to contradict the Captain. Shepard nodded, tensed, turned to Miranda, who nodded, and then bolted.

Immediately, Veetor reacted to his movements, firing at him. Shepard tried weaving between boxes but he needed to remain a target. Fortunately, Miranda was as good as her word - the minute he had set off, she had stood up, hands glowing blue as she did so. A moment later, Veetor's phaser dropped to the ground in front of Shepard, the fall denting the casing.

Veetor, for his part, looked panicked. Now Shepard could get a good look at him, he definitely looked like his suit had suffered some damage. He looked around, apparently considering his options, then he ran back into the prefab. Shepard cursed.

"Shepard to Zorah," he said, taping his combadge. "Veetor ran inside the prefab. We're in pursuit."

"_Roger that,_" Tali replied.

Shepard turned to his team. "Set your phasers to stun. Come on."

They moved, adjusting their phasers as ordered as they did so.

"What you can tell me about the attack?" Shepard asked Tali as they moved.

"_That it was quick,_" Tali replied. "_But me and most of my team were down in the bunker we're hiding in when it happened. You were the first sign that they were gone - before that we had no idea that they might be. We assumed any help might have to fight through them._"

"Who was it?" Shepard asked.

"_There was no way to get a clear reading,_" Tali replied softly, "_and we had no visual surveillance. But whoever they were, they were thorough._"

That wasn't very reassuring, but Shepard shunted that information aside for now. He led his team up a ramp that led into a street - it was totally deserted, but Shepard didn't like the vibes he was feeling from the place.

"Keep alert," he said. His team nodded. A moment later, his combadge beeped.

"_Shepard, this is Zorah,_" Tali's voice spoke. "_Be advised, we think Veetor may be trying to activate the security mechs._"

Shepard turned to Miranda, who helpfully explained. "They're a recent innovation - limited VI security software installed into a robotic body. Quite common on remote worlds with no or limited Starfleet protection."

Shepard nodded, and tapped his combadge. "This is Shepard." He hesitated, trying to think of some way to reassure Tali without giving the game away. "Don't worry, Lieutenant Commander, we've got this."

A moment later, a handful of robotic humanoid figures appeared - their skull-white colour scheme and value skeletal appearance gave them the unsettling look of undead soldiers summoned from the mouth of hell, but Shepard had fought far worse things in his time. The minute the mechs noticed them, they began firing. They seemed to be armed with projectile weapons, judging by the bullet impacts in the ground around them. Shepard and his team quickly took cover, firing pot shots off at the mechs as thy did so.

"Phasers set to stun won't do it," Jacob pointed out. He was across the street from Shepard, behind a crate.

"Yeah, figured," Shepard replied with a grin. He put the type-2 phaser back in his buffer, and got out the TR-116. "Ok then."

He stepped out, aiming and firing as he advanced. The first mech took a shot in the neck and went down immediately. The second took a shot to the chest,n kept firing a moment, then exploded from within. A third mech lost an arm, but kept firing - before it could get more than a couple of shots off, though, a bolt of blue biotic energy flew towards it, sending it flying backwards. Miranda was stood up, her type-2 now clearly set to a stronger setting, judging by the ruby red phaser beam that sliced a fourth mech in half. Orange phaser bolts flew from Jacob's phaser, striking a fifth and sixth mech and blowing them to pieces.

A few moments later, almost as soon as they had arrived, all the mechs were down. Shepard nodded to his team as they continued through the streets.

"_Shepard, this is Zorah,_" Tali's voice spoke. "_I'm tracking your team. Veetor should be in a building on the opposite side of the courtyard directly ahead of you._"

"Roger that," Shepard replied. "Moving now."

He led his team into the courtyard, keeping an eye out for any more mechs. It was a wide open space, which always made Shepard nervous - wide open spaces just begged to be filled with all sorts of hostile enemies.

On the other side of the courtyard was a building with a small platform, upon which Veetor stood. The minute he saw them, he ducked inside the building, tapping away at a tricorder.

"Brace for more mechs," Shepard said to his team, taking cover.

For a moment, there was nothing, and Shepard considered the possibility that he had been wrong about the incoming mechs - not something he'd complain about. Then, there was a soft shake.

"The hell?" he said softly. Jacob and Miranda were looking around for the source of the shake. A second shake occurred. A moment later, there was a third.

"_That crafty bosh'tet!_" Tali said through the comm, sounding equal parts frustrated and impressed. "_Captain Shepard, be advised, you have an inbound heavy mech._"

"Heavy mech?" Shepard repeated, as the ground continued reverberating in what was now unmistakably a pattern of footsteps. "I don't like the sound of that..."

A moment later it appeared, walking out of a large cargo door near the edge of the courtyard - as bone white as the rest of the mechs, but easily five or six times their mass, four times their width, and about twice their height. Each arm was armed with a giant Gatling gun. It scammed the courtyard, and quickly noticed the Starfleet officers.

"_**Target locked,**_" it said in a deep voice. The guns opened fire.

"Shit!" Shepard swore, ducking behind his cover as fire rained in their direction. He turned to his team, who were equally suppressed, "Options?"

"I can create a biotic barrier," Miranda said quickly. "If you are quick, you can line up a high powered shot to its head with a phaser assault rifle. You'll have to be fast though, it won't hold up for long."

"Agreed!" Jacob said. "Sounds like our best option!"

Shepard nodded, getting his phaser assault rifle out and setting it to maximum. "Do it," he said.

Miranda nodded softly, then stood up, her hands glowing blue once more. This time, a semi-transparent field of blue energy appeared, almost like a giant shield between the hail of bullets the mech was firing and the Starfleet officers.

Shepard stood up, concentrating as much as he couldn't in the time allotted. Time seemed to freeze.

He fired one shot - the phaser bolt flew out, striking the mech in the head. The robotic giant seemed to stand still for a moment, as if registering that it had ceased functioning. Then, slowly, it toppled to the ground, the entire courtyard shaking as it did so.

"Well, that wasn't too bad," Miranda said, breathing heavily from biotic exertion.

"It'll only get worse," Shepard said softly. "Of that I'm sure." He tapped his combadge. "Shepard to Lieutenant Commander Zorah. Heavy mech dealt with. Now moving to retrieve Ensign Veetor'Nara. If you and your remaining crew could come meet with us please?"

"_Good work,_" Tali's voice replied. "_On our way._"

Without waiting for her, Shepard stood up, leading his team to the small building where Veetor was holed up.

* * *

Wen the door to the building opened, they found it was only one small room with a large display and a security console. In a chair in for too this sat Veetor, mumbling to himself.

Miranda got a tricorder out and started scanning him.

"From these scans, I'd say he's suffering from extreme traumatic stress symdrome," she said softly. "Explains why he doesn't seem to recognise his surroundings."

"Or the people he's ordering mechs to shoot at," Jacob added, his voice laced with sarcasm.

"We could probably check these security videos, see if there's any footage of the attackers," Shepard mused, looking at the security display.

At that point, Veetor turned around to look at them.

"Who..." he said softly. "Who are you? Why didn't they take you?"

The three officers exchanged glances, unsure how to proceed.

"We've only just arrived," Shepard replied softly after a moment. "We weren't here when the attack happened."

"Then..." the nervous looking quarian said, looking between them, "then you didn't... didn't see them?"

"See who?" Miranda asked, sounding more impatient than understanding. Shepard gave her a look and she shut up, but Veetor was already at his console.

On the display, the images appeared - the same courtyard they had been wandering in just moments ago, this time dominated by a pile of bodies - human bodies. The bodies were carried by metallic figures, that looked almost armoured, but also slightly hunchbacked. Some of them looked more ungainly than others, and some of them seemed to have more organic armour than others, but all of them wandered around the courtyard, bringing more bodies or guarding those that did. There was no sound, and Shepard was immensely glad for that.

"There was a mist," Veetor said, describing what he had seen. "Like... like deep fog... it came, descended onto the planet. Everyone froze... and then they came. Monsters. They took everyone. No - not everyone. The humans. Only the humans."

"Is that a species we're familiar with?" Shepard asked the other two officers. They were staring at the image intently. Jacob looked puzzled, but there was something akin to recognition in Miranda's eyes.

"It looks like... but it couldn't be," she said, eyes wide.

"Like what?" Shepard asked.

"It could almost be a Grigari," Miranda said softly. "But that's ridiculous. This is well beyond their scale or modus operandi."

"Grigari?" Jacob apparently knew the name. "That's crazy."

"And yet," Miranda said, pointing at the image, as if that explained everything.

"I'm sorry," Shepard put in, looking between them, "but what exactly is a Grigari?"

"Advanced alien race," Jacob said. "Legendary. Most people think they're a myth."

"They're no myth," Miranda added, frowning in concentration. "There have been isolated encounters with them over the years. They sell their nanotechnological medicines to planets - but the medicines aren't what they're advertised to be. They're also pirates and scavengers. They're never this aggressive, never this bold."

Shepard sighed, looking up at the image of a Grigari. It was disturbing somehow, but he couldn't tell quite why. He sighed.

"I'll grab the data he collected," Miranda said, moving to download the contents of Veetor's computer. Apparently, the effort needed to speak to the Starfleet officers had drained him, since he was currently back to murmuring to himself.

What were the Grigari doing? Were they somehow connected to the Reapers, or was this some separate invasion? Shepard didn't know, and irritatingly enough all this mission had done was stir up old ghosts and ask more, and far harder, questions.

"Veetor?" an all too familiar voice spoke behind Shepard, shattering his line of thought. He turned in shock, to see Tali and two more Starfleet officers - a Vulcan and an Andorian, both in security mustard - enter the room.

Tali was wearing the same style of environmental suit she had worn the last time Shepard had seen her. It was modified to match the colour scheme of the latest Starfleet style, as was her combadge. Her head-cloth was the same mustard yellow it had been before, albeit slightly more decorated with as subtle pattern now. As she entered, she looked at Shepard, and he could have sworn her eyes widened.

"Shepard..." she breathed, sounding as shocked as the Captain felt. "Captain Shepard. I thought it was just a crazy coincidence but..."

She suddenly aimed her phaser right at his head, her stance angry.

"Identify yourself, now!" she said, her voice calm and even considering what she was doing. Behind Shepard, Jacob and Miranda aimed their phasers, but Shepard had no interest in violence - and he could understand Tali's scepticism all too well. Slowly, he reached to his combadge, took it off his chest, and held it out to her. The phaser stayed aimed at his head for a long moment, and then slowly it lowered, before being out back on her belt. Slowly, she reached out a hand, and after a moment, clasped Shepard's outstretched hand around the badge. A moment later, they were hugging.

"I thought you were dead!" she said, sounding close to tears.

"I kind of was," Shepard replied sheepishly as the hug broke apart. "It's a long story and I was asleep for a lot of it." He turned and pointed at the shaken Veetor. "I found something you lost."

"Yes," Tali said softly. "I can see that."

"Any other survivors besides Veetor and your team?" Shepard asked, getting to business.

"No," Tali said mournfully. "We were fortunate. The majority of the team were up here." There was a pause. "Do you know who the attackers were at least?"

"If Miranda's right," Shepard said, trying to keep the scepticism from his voice, "then it's a race called Grigari."

"Grigari?" Tali said in confusion. "I've never heard of them."

"Join the club," Shepard smirked. He felt happier now than he had since joining this mission - for the first time, he felt like himself again.

Tali paused, as if unsure what to say next. "Shepard - I... I... what's going on? What happened to you? I have so many questions..."

"Captain," Miranda said, interrupting his train of thought, "now that we have this data we should return to the _Eagle_."

Shepard cursed. He wanted to stay - to feel this connection to his old life again - but his duty came first.

"Will you be alright?" he asked Tali.

"We should be," she replied. "I sent a message off to the Exeter. They anticipated arriving within a day or two. We have enough supplies to last til then." She laughed bitterly. "A colony's worth, in fact." She paused again. "Take care, won't you?"

"We will," Shepard replied. "As much as ever."

"Uh huh," Tali replied, amusement in her voice. "So you'll get blown up again."

"Quite possibly," Miranda cut in, frowning. Before Shepard could say anything else, she tapped her combadge. "Eagle, this is ground team - three to beam up."

Shepard looked back at Tali, just in time to see her and the rest of the room dematerialise...


	5. USS Cerberus

**AN: The Grigari, in response to the guest reviewer, are a race from several Star Trek books. They use nanotechnology, are basically a race of rather disturbing walking nanotech-powered corpses, and are generally unpleasant. I decided to use them because very little is "canonically" known about them and they're a Star Trek race, so replacing the Collectors with them seemed an interesting twist on something not much is known about.**

**Anyway: sorry it's taken a while for me to get back into this. Unfortunately the spurt of fast writing that saw me through the majority of the first story and the first few chapters of this one has - quite clearly - ended, and real life has returned with a vengeance. I've had moving stuff from a house into my flat, a job interview, some filming and thinking about when I return to uni to think about. In any case, I'll do my best to update when I can, but it isn't going to be something I can regularly schedule.**

**Also, apologies for the comparative shortness of the chapter. It was a filler chapter, and said all I needed it to say quite quickly.**

* * *

**Chapter Four: USS ****_Cerberus_****.**

Shepard cursed softly as he rematerialised back in the transporter room of the _Eagle_.

There had been a lot he might have wanted to say to Tali given the chance - and even leaving those sort of things out, it had been nice to just be in the company of a friend again, to feel like he was himself, even if it was just for a few short minutes. Instead, he hadn't even had a chance to say goodbye. Again.

He threw Miranda, who was standing to his right, a dirty look, but she was already marching off of the transporter pad, apparently perfectly content with what had just happened - or at least, not feeling terribly guilty about it.

"That must have been awkward for you," Jacob said sympathetically from Shepard's left. The Captain turned to look at the security officer, who seemed sincere enough in his concern. "Are you ok?"

"I will be," Shepard replied softly, and Jacob nodded.

"It'll get better," the other man said with a grim smile. "Give it time. These things always get easier."

"I hope you're right," Shepard sighed. Without another word, he walked out of the transporter room, trying to convince himself that he hadn't just told a blatant lie to Jacob.

Truth be told, he wasn't ok, and he couldn't see any way that he would be any time soon, given time or anything else. Being yanked away from that connection was the worst possible thing that could have happened to him in his state of mind. He had needed to feel like himself, but... instead he just felt more alienated.

His combadge beeped, shaking him out of his train of thought.

"_Shepard, this is Harper,_" the grizzled voice of the Section 31 Admiral spoke. "_Please report to my ready room to give your mission report in person."_

Shepard sighed, and tapped his combadge.

"Shepard here," he said softly. He briefly considered telling Harper to go fuck himself. "I'm on my way."

It seemed there was no rest for the wicked. Or for that matter, Shepard mused bitterly, no sleep for the dead.

* * *

Harper was looking extremely thoughtful. Shepard had told him everything he had discovered down on Freedom's Progress, right down to the revelation that the Grigari were supposedly the ones behind the attack, and the Admiral had just sat there and listened to everything, taking it all in and musing on the information.

"Grigari," he murmured thoughtfully once Shepard had finished speaking, looking somewhat troubled. "Grigari. Now that's a name you don't hear around these parts too often. Why now, I wonder?"

"They are real then?" Shepard asked, still very sceptical about the whole thing.

"Oh, yes," Harper said, looking none too happy about it. "Real and horrifyingly dangerous. Their nanotechnology is some of the most advanced around, but it's gruesome stuff."

"In what way?" Shepard asked.

"I'm not the right person to explain it to you," Harper said, frowning thoughtfully. "But I know of one man who might be able to give it the... detail it would need. A Salarian scientist named Mordin Solus, currently working on Omega." Harper paused, and nodded. "Yes, Solus is a good place to start. You'll need his help anyway, in order to develop some kind of countermeasure to this 'paralysing mist' described in the intel you collected."

"You talk as though I'm definitely helping you," Shepard frowned, folding his arms, "but I seem to recall saying I'd help you only if the Reapers were involved. I found nothing down there to suggest their involvement in any way."

"But you found nothing that conclusively disproved it, either," Harper pointed out. "For all you know, the Reapers are working with the Grigari the way Sovereign worked with the Borg."

"Somehow I doubt that," Shepard said scathingly. "If there's nothing else, I'd like to be dropped off at the nearest Starbase to be given my next orders."

Harper sighed softly, as though pained by Shepard's words. "I didn't want to do this Captain, believe me on that, but you've forced my hand."

At Shepard's incredulous look, the Admiral picked up a PADD from his desk and handed it to Shepard. The Captain read the writing, the frown on his face getting deeper and deeper as he did so.

_To John Shepard, Captain,_

_This message confirms your official status as being returned to "alive", and your medical status as being "fit for duty"._

_You are hereby requested and required to serve as part of the Starfleet Reaper Research-And-Combating Task Force, under direct command of Admiral Jack Harper._

_Signed,_

_William Ross, Admiral._

"This is bullshit," Shepard said after a moment, looking Harper directly in the eye.

"I'm afraid not," the Admiral replied, smirking at the Captain's colourful language. "You're under my direct command, Captain Shepard. That's 'where Starfleet wants you', as you put it."

"And you manipulated that outcome," Shepard accused him.

"Believe what you want," Harper replied nonchalantly. "It doesn't change these fundamental facts" He leant forward, speaking animatedly. "Federation colonies are being attacked, by the Grigari, who might be working with the Reapers. Even if they aren't, it's still a major threat. You are a Starfleet officer - your duty, whether under my command or someone else's, is to stop the Grigari. I'm offering you assistance in doing that."

He had a point, and even if there was no Reaper involvement, Shepard could still see why the Grigari were a threat to galatic safety, and having the resources of Section 31 - copious as they seemed - was a very tempting position to be in. Still, he had nothing but anger about this entire situation. He tried to restrain himself from saying anything to an Admiral that he might later regret.

"I want it on record that I was made to take this assignment to your command against my better judgement," he settled with finally. "Sir," he added, making it an insult.

"Objection so noted," Harper said, still smirking in that infuriating way. "However, just because you report to me doesn't mean I'll be watching over your shoulder, so you needn't worry about that. You'll be given your own ship, your own crew, a guideline or two and some intel to help you out. Other than that, the mission's yours."

"Limited oversight?" Shepard asked. "Like Reed on Feros?"

"Less so than Reed," Harper smiled, clearly trying to be friendly and reassuring and failing on both counts. "He's a weapon, a tool. You're a Captain, and you know about Reapers. You've earned yourself a lot of leeway in my book."

"I'm glad you think so," Shepard said dryly, deciding to to point out that he probably didn't have the leeway to tell Harper to piss off. "So what ship am I getting?"

Instead of replying directly, Harper pressed an intercom control.

"Lieutenant Reed," he said, "get up here please." At Shepard's raised eyebrow, Harper sighed. "I did tell you, you're going to have to get used to working with Reed. He's a fine officer, once you ignore his sense of humour."

"I don't trust him," Shepard replied.

"You should," Harper said. "If there's one person on your roster who's going to respect your decisions without questioning them, just on principal, it's him."

At that moment, Reed arrived, forestalling any reply on Shepard's part. He was still dressed in the leather jacket over the duty uniform shirt, though he had apparently had time to smarten his hair up a tad. He came crisply to attention in front of Harper's desk.

"Sir," he said sharply.

"Reed, the Captain's new command should be arriving in-system shortly," Harper said briskly. "I want you to show her to him, inside and out, and have her ready to depart."

Reed smiled slightly. "Yes sir." He turned to Shepard. "If you'll follow me, Captain."

He walked out. With a last look at Harper, who smiled softly, Shepard followed.

* * *

On the bridge of the _Eagle_, the dark haired Commander Leng turned to look at the two of them, eyes narrowing at them in something resembling contempt.

"She's about two minutes from rendezvous," he said, his voice quiet and grim. "Be glad to have you off my ship, Reed."

"Not as glad as I'll be to be far away from you, Leng," Reed replied snidely.

Shepard vaguely wondered what had caused the antagonism between Leng and Reed - and Miranda, he remembered. It was definitely strange - most officers transferred to different commands if they found they genuinely couldn't work with someone... then again, that might not be possible in Section 31.

Saying that, Reed apparently was transferring to a different command. Namely, his command. It was a little disconcerting to know that his own personal preferences of who exactly got onto his ship were being essentially ignored. Still, he would have to deal with that fact.

Shepard was distracted from his line of thought by Commander Leng speaking.

"_Cerberus_ decloaking now," he said.

A small ship appeared on the viewscreen. It's lines were unlike any other Starfleet vessel, with no saucer and no protruding nacelles, small and compacted - it was a _Defiant_ class, the only Federation ship class designed solely for war.

"Well," Shepard said softly, inspecting the lines of the ship as it flew closer to the _Eagle_. "That is... not what I was expecting."

"You think we were gonna give you another _Ambassador_ class clunker?" Reed said derisively, and Shepard suppressed the urge to punch him. "Nope - the _Cerberus_ is sleek, smooth, fast, and doesn't have any distractions fitted. No bullshit science labs - she's a predator."

His voice was filled with a kind of awe. To Reed, this kind of ship was something beautiful, something he could look at as the pinnacle of engineering and be thrilled to work on. To Shepard, she was at best a sad necessity and at worst a dangerous diversion from what Starfleet should really be doing, and he didn't want to serve on one, let alone command one. Nonetheless, here he was, left with no choice in the matter.

"They're hailing," the _Eagle's_ tactical officer said.

"On screen," Leng said. A moment later, a face Captain Shepard had never expected to see again appeared.

"_Eagle, this is USS_ Cerberus," Lieutenant Jeff Moreau - Joker - said in greeting, a wide smile upon his bearded face. "_We're ready to receive Captain Shepard._"

* * *

A few minutes later, Shepard - together with Miranda, Jacob and Reed - materialised in the transporter room of the USS _Cerberus_. Joker - together with a grizzled, scarred man and a young Asian woman, both in operations mustard - was waiting for him, arms folded.

"Well you look better than I expected," the pilot said to Shepard with a wide grin.

"I feel better than I might have expected, too," Shepard replied, his grin matching Joker's inch for inch. He stepped down from the pad and shook his old friend's hand, shocked to see him again. "Can't believe you're working for Section 31."

"Got the orders to transfer to USS _Cerberus_ a few weeks ago," Joker replied. "She handles like a dream, by the way. The whole Section 31 thing kinda snuck up on me though, they didn't tell me until after I was already here."

Miranda, standing behind Shepard, coughed slightly.

"Oh, shit, yeah!" Joker exclaimed, before turning to the other officers who had been with him. "This," he said, indicating the scarred man, "is Lieutenant Zaeed Massani, security and weapons specialist."

"Pleasure, Captain," the man said with a nod, his voice gruff and hard-edged.

"Likewise," Shepard said, shaking the man's hand. He had a firm grip, and seemed almost to be testing the Captain.

"And this is Ensign Kasumi Goto, requisitions and intelligence," Joker continued, indicating the woman. She smiled and held out a hand. As Shepard shook her hand, he touched she had the rank insignia of an enlisted officer, not a full Starfleet graduate. He made a note to ask her about it later.

"Pleasure to be working with you on this," she said, her voice warm and full of enthusiasm.

"Again, likewise," Shepard said, smiling. "Requisitions and intelligence? Seems an odd combination."

Kasumi winked at him. "You'd be surprised how often the two seem to go together."

"I'm sure," Shepard smiled. He turned to Joker. "I guess you have a ship to show me."

"I guess I do," Joker smiled. "Come with me, boss."

"We'll head to our assigned stations," Miranda said from behind Shepard. "You'll find a full duty roster in your cabin to look over."

"Thanks, I'll bear that in mind," Shepard said, almost dismissively, as he and Joker left the transporter room.

"You don't like her much?" Joker asked.

"Not really," Shepard replied, "though I'm sure it'll work out, somehow."

"Stuff usually does," Joker noted. The two of the continued walking down the hallway. "Anyway, the Cerberus is a lean little ship - no holodecks, very little in the way of recreational facilities, but she's got the best and most up to date defensive systems in Starfleet."

"I suppose we should expect no less from Section 31," Shepard said grimly, as they stepped into a turbolift.

"Yeah," Joker said. "Bridge," he added, speaking to the lift.

A moment passed in silence as the lift ascended.

"Computer, halt," Shepard said suddenly. The lift halted, and Shepard turned to face Joker.

"Something on your mind sir?" he asked, frowning in confusion.

"Section 31," Shepard replied. "I want your opinion."

Joker's frown deepened. "If you're asking for my loyalties, sir," he said, sounding almost offended, "they go you, my friends from the _Normandy_, Starfleet, the Federation, my own ass, the average amoeba, and then Section 31."

"I knew that," Shepard said, brushing the question of Joker's loyalty aside - that had never been in doubt, as far as the Captain was concerned. "I mean, do you trust them?"

"Depends," Joker replied, sounding moderately happier now he knew what Shepard meant. "I trust that they mean to help the Federation, but they've got some pretty screwy ideas about what constitutes morality, acceptable behaviour, means and ends, that sort of thing." He paused. "I don't trust them not to screw us over the first time they need to, but I trust that they won't screw us over while they need us."

"My thoughts precisely," Shepard nodded, his face thoughtful. "You and I, as of now, are the only people left from the _Normandy_. Worst comes to the worst, I need to know you have my back."

Though he was sure the Captain meant in a combat situation, and though he knew he wasn't going to be much use if that happened, to his credit, Joker didn't hesitate before replying. "In a heartbeat, Captain."

"Good," Shepard said, smiling, "now that's settled, Computer resume turbolift." He sighed. "Time to meet the crew."

This would be... interesting.


	6. The Crew I Never Asked For

**Chapter Five: The Crew I Never Asked For**

The bridge of the _Cerberus_ was bigger than Shepard had been expecting from such an economically designed ship - it was at least the size of the old _Ambassador_ bridge, if not bigger. The helm, tactical and Ops consoles lined the walls at the front of the bridge rather than being isolated in the middle of the room. There were auxiliary stations at the back where junior officers stood, and more lined into the wall, each one displaying tactical status reports and other combat minutiae, and Shepard had no doubt that any one of those stations could become an auxiliary tactical, helm or Ops station the minute the primary one was disabled. It was, in short, a ship designed for war, just as Shepard had expected.

He walked over to the command seat, Joker standing next to him with a sort of worriedly expectant half smile on his face, like he wasn't sure whether Shepard was alright. Shepard didn't know what to tell him - he wasn't alright, really. Seeing Joker again was a positive, but it was only one thing against a pile of changes he wasn't sure he liked.

A woman with blonde hair set into a neat bob walked up and stood to attention in front of him, disrupting his thoughts. Though she wore an operations uniform, she had no rank insignia. Shepard couldn't help but notice that there was something off about her gait - it was too stiff, almost mechanical.

"Captain Shepard," she said, her voice oddly stilted. "Welcome aboard the USS _Cerberus_. I am the Enhanced Defensive Intelligence Hologram..."

"Yeah, yeah," Joker said, cutting her off with a wave of his hand and a derisive snort at the title. "This is Edi, short for that dumb acronym she just spouted - we usually drop the H, or it'd sound weird." He gave a crooked grin. "She's our emergency support system. She also talks too much, but in general she's ok."

"Emergency support system?" Shepard repeated.

"I am, as I said, a hologram," Edi replied. "Based on an experimental design from Lewis Zimmerman. During combat situations, I am linked into the tactical systems to provide improved response time between a situation developing and the Captain being informed. This updates the Captain with an estimated ten to twenty percent reduction in delay."

"So if critical systems are damaged, I know faster?" Shepard asked, and Edi nodded. "What if the holoprojection system is damaged?"

"She has a portable holo-emitter installed," a stern voice cut across the conversation, and Miranda walked up to the group. "Captain. I'll be serving as your XO for this mission."

"Very good Commander," Shepard replied coolly. "I was just acquainting myself with Edi."

"It's impressive technology," Miranda said.

"Yeah, _she_ is," Joker put in, frowning at Miranda slightly. "Anyway, I've got a ship to fly."

He walked over to the helm, leaving Edi, Miranda and Shepard by the command chair.

"He's a bit sentimental, isn't he?" Miranda asked Shepard, raising an eyebrow slightly in an almost Vulcan way.

"He's one of the best officers I've ever served with, Commander Lawson," Shepard replied, his voice lowering by degrees. The other officer's eyebrows both shot up into her hairline.

"Very well, Captain," she said shortly. "If you'll excuse me, I have duties to perform."

With that, she walked off, leaving Edi - still stood at attention - with Shepard. The Captain slumped into the command chair - the moment of first sitting in a new ship's command chair completely passing him by - wondering how else he was going to screw up today.

"Is there anything I can help you with, Edi?" he asked the hologram.

"No sir," she replied. "Do you require anything at present?"

"Not right now, no," Shepard replied. He thought for a moment. "I'll speak with you later regarding optimal use of your functions, just so I know when to call on you."

"Yes sir," the hologram said with a nod. "If you'll excuse me."

She walked off, leaving Shepard shaking his head. If that didn't beat all - a holographic crewmember.

"Captain," an officer at the Ops console said, interrupting his thoughts. "Admiral Harper on Eagle is hailing."

"On screen," Shepard replied immediately, sitting up slightly.

Harper's face popped into view on the front screen, clearly still sat in his ready room.

"_Captain,_" he said. "_How is she?_"

"The Cerberus is well put together, Admiral," Shepard replied, faking professional enthusiasm as best he could. "I'm looking forward to taking her for a spin."

Harper didn't look like he believed Shepard, but he wasn't questioning him on it either. "_As I said, Captain, Professor Mordin Solus on Omega is a good place to start when searching for ways to combat the Grigari. I'd advise starting there._"

"Good advice," Shepard nodded. He didn't really like to say so - he didn't really want to seem like he agreed with anything in this situation - but he did think the idea was sound. If these Grigari had such advanced tech, then defeating them required brilliant minds. "I'll set a course immediately."

"_See that you do,_" Harper said. "_Other than that, you have free reign to combat the Grigari threat and investigate their attacks as best you can. Good luck, Captain._"

"Thank you, sir," Shepard replied, and then Harper disappeared, leaving the view of the Eagle. After a moment, the other ship cloaked, vanishing into the blackness of space.

"Joker," Shepard said. "Set course for Omega. Relay and maximum warp."

"Aye sir," Joker replied, inputting commands on his console. "Course set."

"Engage," Shepard said. A moment later, the familiar feeling of FTL travel hit him - the subtle shift in the way a ship felt - and he knew they were underway. "I'll be in my ready room."

He stood up and turned to go, but nearly ran into a diminutive woman with short hair in an operations uniform. She was young - very young - and she held a PADD in her hand.

"Captain!" the woman exclaimed, standing to attention. "I'm Yeoman Kelly Chambers. I'm in charge of your personal messages and crew rosters."

"Yeoman," Shepard said with a soft smile. "I need you to do me a favour - I'd like to arrange meetings with Commander Lawson, Lieutenant Taylor and Mr Reed on our journey to Omega."

"Yes sir, I'll arrange that immediately!" Chambers said chirpily. "And may I say, it's an honour to be serving with you, Captain."

"I'll try to live up to that," the Captain replied, sounding vaguely tired. With that, he headed for his ready room. Chambers started making notes on her PADD, a thoughtful frown on her face.

* * *

The ready room was bare and unpersonalised, and Shepard had no intention of fixing that any time soon. He sat down in his chair, leant back, and sighed. He was filled with a kind of ennui, and felt like every decision he was making, every action he was taking, was just him coasting along, almost running on autopilot. That had to change. Too much was riding on him. Shaking his head and trying to clear his feelings of despondency, he activated his computer and began entering search parameters for the Grigari - he needed to know everything.

As it turned out, there wasn't much to go on. They occasionally acted as mercenaries it seemed, but so little was known about them that anything he found could at best be labelled conjecture. There must have been more to it though...

An hour passed as he researched, when his door beeped.

"Come in," he called.

Miranda Lawson walked into Shepard's ready room, standing to attention before his desk. Shepard turned his computer off, and nodded at her.

"Commander Lawson," he said in greeting, trying his best to sound friendly. "I'm glad you could make it."

"Indeed," Miranda said, frowning slightly. "I should warn you sir, if this is an attempt to socialise with me or get to know me, I usually prefer not to do that on assignments."

"I need to know my crew, Commander," Shepard replied, his voice cooling slightly. "I need to know I can trust you. Especially since I didn't pick this crew and didn't pick this assignment.'

Miranda seemed to consider this. "Alright then," she said finally. "That seems fair enough. What would you like to know?"

"Your service record seems fairly nondescript prior to what I assume is the start of your Section 31 career," Shepard began. "Biotic corp, usual damn fixing, emergency support at disasters, other such things. What's interesting is that you gained most of your promotions following the 'assignment to Admiral Harper's staff'."

"I did certain operations for Section 31," Miranda replied. "That is all on a need-to-know basis. Suffice it to say the Admiral was impressed, hence my current assignment."

"He trusts you with his most important missions then?" Shepard asked.

"He trusts me to get things done," Miranda replied bluntly, surprising Shepard. "Others said you couldn't be revived. I got it done, with the best team the fleet could assemble. Now he trusts me to keep you alive so that you can get things done."

"So you're a bodyguard, as well as an XO," Shepard said uncertainly.

"I have a wide range of objectives," Miranda replied. "The completion of this mission, your survival, the rest of the crew's survival."

"Seems a lot to place on one person's shoulders," Shepard commented. "I'm sure you're more than competent, but you're only one officer."

"I am an exceptionally good officer," Miranda replied evenly, "with exceptional skills and abilities. I can do whatever is asked of me."

"Would 'lightening up' come under that?" Shepard asked with a wry grin. Miranda gave a small half smile.

"I can certainly try sir," she replied. "Now if that's all."

"Dismissed," Shepard said with a nod.

* * *

Shepard sat back in his chair as Jacob Taylor walked in and stood to attention.

"Mr Taylor," Shepard said with a smile. "Just been going over your service record. All exemplary."

"Just doing my duty, sir," Jacob said modestly. "Any officer would."

"I doubt any other officer has quite this kind of service record," Shepard said. "Repeated frontline actions aboard USS _Sussex_ during the Dominion war. Special commendations for bravery, good tactical thinking and a dozen other similar remarks all paint quite the picture."

Jacob stood there, waiting for Shepard to finish. He seemed somewhat uncomfortable being reminded of his accomplishments.

"Your record seems the textbook definition of spotless," Shepard summed up. He leant forward slightly. "Begs the question - you're working or Section 31. Why?"

Jacob shrugged. "Got assigned as the tactical officer of that station by higher ups. The Sec 31 element didn't come up until later."

Shepard nodded. "And if I asked you what you thought of the organisation?"

Jacob looked a little uncomfortable at that.

"Off the record, sir?" he asked.

"Entirely," Shepard assured him.

"Then, I don't know if I like the organisation's methods," Jacob said immediately. "The mandate is fine - defending the Federation is what I signed up for after all. But doing it the way these guys do it - the secrecy, the covert ops, the freaky missions like that Thorian thing - that's different."

Shepard smiled.

"I believe we're on the same page, Mr Taylor," he said.

"Good to know sir," Jacob nodded. "I want to say, I'm honoured to be serving with you on this mission."

"The feeling is mutual, Mr Taylor," Shepard replied. "Dismissed."

* * *

When Reed walked into Shepard's ready room, he was in full duty uniform, looking for all the world like the most respectable Starfleet officer you could imagine. Perhaps this was partly due to some desire to make a good impression - as if he had a chance in hell of doing that, Shepard thought to himself, but he quickly dismissed that thought. He had to work with the man, so he needed to give him a fair chance.

Reed stood at parade rest in front of Shepard's desk, waiting for his Captain to speak.

Shepard sighed, deciding to offer an olive branch.

"At ease, Reed," he ordered softly.

The man hesitated for a moment, then relaxed.

"You wanted to see me, sir?" he asked.

"I like to know my crew," Shepard replied. "And let's be honest, our previous interactions prior to this assignment were... troublesome. I need to know I can trust you."

"To follow your orders?" Reed asked, sounding vaguely offended at the idea that he might not. "I have two pips. You have four. End of that discussion."

"Is it?" Shepard asked, not a little sceptical.

"You're my superior officer, Shepard," Reed replied, sounding deadly serious. "I'll follow your orders to the letter, whether they be naive, or I disagree with them, or even if they're just plain stupid. It's what I do, and what I have done all my career."

Shepard nodded slowly, accepting the man's word.

"Alright," he said, leaning back in his chair. He motioned for Reed to take a seat, and the Section 31 agent did so. "Been meaning to ask. That synth-leather jacket of yours, the names on it. Campaigns you fought in?"

Reed smirked slightly. "Yeah, that was a custom uniform design a few veterans got made. Me, Jacob, a bloke called Reese, a few others. The names are the battles we survived - leastways the ones I could talk about. I performed a few commando raids on Betazed, frontline on AR-558, and served on the USS _Eagle_ for the fleet battles at Chin'toka and Cardassia, plus being part of the ground landing on Cardassia as well, though that was thankfully truncated. Others did lots more. Being Sec 31 kept me off of the frontline most days."

"I thought about reading up on the war," Shepard said slowly, "but I want to hear it from someone. What was it like?"

Reed hesitated, looking faintly uncomfortable. "Other people could tell you."

"I didn't ask them," Shepard pointed out. "I asked you."

Reed, to his credit, nodded. "Alright then. How much do you know about the Dominion?"

"Less than I should," Shepard replied. "Most of my intel was old, and I didn't keep up to date. Too focused on the Reapers and Borg."

"Which was fair enough at the time," Reed replied. "So I guess you wouldn't know much about the Founders?"

"Shapeshifters, yeah?" Shepard asked, frowning as he thought back to old briefings about the strange alien race.

"Yup," Reed nodded. He leant back in his chair, seemingly thinking about what he was going to say. "The Founders were highly intelligent, highly advanced. No one knows quite how, but they genetically engineered themselves several servant races - the Jem Hadar, the Vorta - and formed an empire."

"The Dominion," Shepard nodded.

"Right," Reed said. "There was a big thing about them a few years ago when the _Odyssey_ was destroyed. Dunno if you remember all the crazy hype about shapeshifters invading Earth and what have you, but people were tense. Fortunately, we had the saving grace that the Dominion had never developed relay tech."

"Any idea why?" Shepard asked.

Reed shrugged. "Best anyone could tell, they preferred using tech they had developed themselves or had been developed by their vassals, not tech developed by some dead 'solids'. They relied on their own ingenuity exclusively."

"So how did they become a threat over here?" Shepard asked. "Relay tech is the only way to travel long distances that quickly."

"Bajoran Wormhole," Reed replied. "Stable wormhole, right between us and them. Became both our saving grace and our worst weakness. Saving grace because the thing bottle necked their invasion. Worst weakness because we kept needing to defend the entrance."

"Miranda mentioned that DS9 was captured," Shepard noted.

"It was," Reed said."Opening move of the war."

"Our Alliance with the Citadel held them back from attacking us before," Shepard pointed out. "I take it that didn't hold up?"

"You kidding?" Reed smirked. "The Dominion would probably have attacked eventually anyway. The fact that the Borg caused so much damage - dozens of Starfleet and Citadel ships destroyed - was just the icing on the cake." He paused, thinking back. "They launched ships in a simultaneous wormhole attack combined with help from their Cardassian allies. DS9 fell in a day. We just weren't ready - the crew at DS9 managed to launch a minefield to block off the wormhole so they couldn't get any more reserves in the end, but that was it."

"What happened after that?" Shepard asked.

"It was... pretty back-and-forth," Reed said slowly. He held up his hands, as if trying to visualise what he was saying. "It was like this. They were pushing along every front. The Federation didn't have enough ships, so the Fleets were moving constantly, trying to shore up gaps. Eventually, good leadership got us back on the offensive, and then we managed to spare enough ships to use the Mass Relays as a counter offensive weapon, hit them right in their home territories. Once they realised the Mass Relays were able to bypass their defences they started using them counter-offensively - the Cardies, and then the Breen, raided some inner worlds. Course, the minute the Dominion started using Relays, the Citadel Council shat on them - the turians didn't forget Palaven in a hurry. We got tons of support from them. Add to that a big push that besieged Cardassia - and the Cardies figuring out that the Dominion were their slave-masters not their partners - and I guess it got to the point where the war was too much trouble for the shell-heads and their masters to keep fighting. So they withdrew from the Alpha quadrant, and rumour has it they wrecked every Relay they had in their systems to keep us and the turians out." Reed paused. "That's... a simplified view, Captain, but it's essentially correct."

There was a long pause, during which the two men sat in silence, the Captain registering everything the other man had said to him.

"What was the war like?" Shepard asked finally. "To live through I mean."

The events Reed had described were factual, events he could have gotten from a textbook, though Shepard was happier having gotten them from someone who was there.

"What was it like?" Reed repeated. He leant back in his chair, his eyes taking on a faraway look. "I was on AR-558 for weeks. During that time, we lost over a hundred officers to enemy action. We lost twenty more in the final push before we were rotated out. It was a nasty, brutal thing."

"I'd have thought you were used to nasty brutal things, Reed," Shepard said, perhaps slightly unkindly. "What with your work for Section 31."

Reed gave Shepard a look. "If you called me in here for crotch shots, Captain, I'd rather you didn't. And don't make light of the war - you'll make yourself pretty unpopular."

"Don't worry," Shepard said with a wry grin. "Last crotch shot." He paused, thinking of how tout into words what he was thinking. "I don't like you, Reed, and I'm not sure I trust you, but I'm convinced that despite the stuff you've done with Section 31 you're an essentially decent officer: even if I find your methods questionable, your motivation isn't. Therefore, I'm amenable to working with you. But this is my ship - and you don't do anything on my ship that's wouldn't do, regardless of Section 31's idea of acceptable mission parameters. Clear?"

"Crystal, sir," Reed replied coldly. "And thank you for being honest with me. Permission to be dismissed, sir."

"Dismissed, Lieutenant," Shepard said. Without another word, Reed turned and left the room.

Shepard sighed - now that he had ascertained a little more about the Section 31 officers under his command, it was time to see about this mission he had been given. Despite searching through databases in-between meetings, Shepard had yet to find anything concerning the Grigari that he could call "concrete information" (though a lot of it was classified), and that bothered him far more than he cared to admit. He had a brief think about what he might be able to do, and an idea hit him.

He tapped up his personal message system, and he wrote a message addressed to an old friend.

_To: David Anderson._

_Subject: I'm back+Need help chasing info._

_Don't know what you know about this, but I'm not dead._

He felt ridiculous writing that, but he didn't know how one was meant to frame this sort of thing.

_Also don't know how much I can tell you if you didn't know. Not why I'm dropping a line however,_

_I need information concerning the Grigari. Anything and everything in the most classified files you can get me. I have scraps but need a bigger picture. _

Shepard paused, unsure what to put next.

_I know if you didn't know I was back this will be a shock. It was to me, too. All I can say is, I need that information._

_I hope to hear from you soon,_

_John Shepard, Captain._

He sighed, and sent the message. He didn't know how his old friend would react to it, but hopefully he would accept it and, more importantly, get that information to Shepard in time for it to make a difference.

"_Captain,_" a voice interrupted his thoughts. It was Joker. "_We're coming up to Omega now, sir._"

"On my way," Shepard replied. It was time to see whether this Mordin Solus was as capable as Harper thought he was.


End file.
